A Mechanistic Framework of Genetic Liver Diseases: From Developmental Defects to Functional Disorders

Abstract

Genetic liver diseases encompass a heterogeneous group of conditions that disrupt hepatic development, structure, or function. Advances in high-throughput sequencing have revealed the molecular basis of many disorders previously defined only by clinical or biochemical features, transforming diagnostic and therapeutic approaches. This review proposes a mechanistic framework that distinguishes diseases arising from developmental abnormalities from those caused by functional impairments in hepatocellular or biliary physiology. It outlines how defects in transporters, enzymes, signaling pathways, intracellular trafficking, and mitochondrial function converge to produce diverse hepatic phenotypes. Moreover, translational aspects are discussed such as how the growing integration of genetic testing into clinical practice enables precise diagnosis, informs prognosis and therapy, and refines disease classification. Finally, the review discusses future directions in the field, emphasizing the role of multi-omic approaches, organoid modeling, and data sharing in elucidating unresolved pathogenic mechanisms and advancing precision hepatology.

1. Introduction

The liver is a remarkably complex organ with a central role in metabolism, detoxification, immune regulation, and systemic homeostasis. Its function depends on the coordinated activity of multiple cell types such as hepatocytes, cholangiocytes, Kupffer cells, stellate cells, and endothelial cells, each performing distinct yet interdependent physiological tasks.

The global prevalence of liver disease continues to rise, driven by a broad range of underlying etiologies. The most common causes of liver dysfunction in adults are environmentally derived (i.e., metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD), viral infections [1]) or autoimmune, whereas younger patients are more commonly affected by genetically determined disorders that typically manifest within the first decades of life [2,3,4] (Figure 1).

When genetic disorders are concerned, the pathogenetic process can originate from defects affecting any of the numerous molecular pathways that sustain hepatic function. Advances in high-throughput sequencing and genomic medicine have profoundly expanded our understanding of liver disorders [5,6], revealing that many conditions once defined by their clinical or biochemical phenotype have an identifiable genetic basis.

Genetic liver diseases encompass a wide range of entities, from early-onset syndromic disorders to metabolic, cholestatic, and mitochondrial diseases presenting in childhood or adulthood. These conditions differ in prevalence, inheritance, and clinical severity, yet they often share overlapping biochemical signatures such as cholestasis, steatosis, and progression to chronic liver disease (CLD) or organ failure requiring liver transplantation (LT) [7]. The growing number of identified disease-associated genes has highlighted the need for rational frameworks to interpret their underlying mechanisms and to guide accurate diagnosis and management.

Several approaches can be used to classify genetic liver disorders, either by clinical features, inheritance patterns, or the pathological mechanisms driving tissue injury. However, a number of disease-associated genes exert effects across multiple biological domains, and proteins can have pleiotropic activities or still-undiscovered functions. This can give rise to complex clinical phenotypes that reflect the disruptions of multiple cell functions or result in overlapping clinical presentations.

Moreover, hepatocytes display marked transcriptional specialization along the porto-central axis [8] and thus some genetic disorders preferentially affect specific compartments, although disease progression ultimately involves the entire organ. As an example, defects of urea metabolism, alpha-1 antitrypsin deficiency, and iron handling predominantly impact periportal hepatocytes [9,10,11], whereas defects in drug metabolism, bile acid transport, and copper handling mainly affect the pericentral zone [12], and midzonal hepatocytes appear particularly relevant in conditions associated with impaired liver regeneration [8].

Despite this biological interconnectedness making rigid categorization difficult and potentially misleading, a mechanistic classification could provide a particularly informative perspective, as it directly links molecular dysfunction to hepatic physiology. Thus, genetic liver diseases can be divided into two main categories: those arising from defects in liver development or anatomical structure, and those resulting from functional impairments in hepatocellular or biliary physiology (Figure 1B).

This review explores these two groups in detail, focusing on how specific molecular lesions disrupt liver function and can help in guiding treatment, predicting complications and informing family.

2. Diseases Caused by Developmental Defects or Anatomical Anomalies

Within this category, the most common conditions are ciliopathies and particularly ductal plate malformations (DPMs). Ciliopathies are diseases caused by defects in the primary cilia, which are present in most cells and are not motile (in contrast to cilia present in specific cells such as respiratory epithelium, fallopian tube epithelium, ependymal cells and sperm whose defects cause a specific class of ciliopathies called ciliary dyskinesias).

These disorders primarily affect the portal triad and canal of Hering, thus impairing bile duct development, ductal remodeling, and epithelial differentiation. Because the canal of Hering serves as both a biliary–hepatocytic interface and a progenitor niche, its disruption results in defective regeneration and exaggerated ductular reactions, explaining the early onset of fibrosis in these conditions.

Details about the causative genes associated with these conditions are reported in

Table 1. List of the most common genetic liver diseases affecting cholangiocytes with normal development of the liver. For each disorder, the associated genes and the degree of liver involvement are reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Gene	Liver Involvement	Ref. N.
Congenital hepatic fibrosis	PKHD1	Hepatic fibrosis (cholangiocyte ciliary dysfunction)	[13,14,15,16]
Polycystic liver disease	PRKCSH, SEC63, LRP5, ALG8, ALG9, GANAB, SEC61B, DNAJB11, PKHD1, PKD1, PKD2	Liver cysts with no functional impairment (cholangiocyte ciliary dysfunction)	[17,18,19,20,21,22,23]
Alstrom syndrome	ALMS1	Hepatomegaly, hepatic steatosis, chronic active hepatitis (ciliary signaling defects)	[24,25,26,27,28,29]
Bardet–Biedl syndrome	ARL6, BBS1, BBS2, BBS4, BBS5, BBS7, BBS9, BBS10, BBS12, CEP290, MKKS, MKS1, TRIM32, TTC8	Biliary abnormalities with periportal fibrosis, biliary cirrhosis, and portal hypertension (cholangiocyte ciliary dysfunction)
Biliary Atresia Splenic Malformation (BASM)	PKD1L1	Biliary atresia (abnormal bile duct morphogenesis)
Biliary, renal, neurologic, and skeletal syndrome	TTC26	Hepatomegaly, neonatal cholestasis, ductal proliferation, fibrosis and cirrhosis (ciliary dysfunction)
COACH syndrome	TMEM67, CC2D2A, RPGRIP1L	CHF, cirrhosis, bile duct dilatation, hepatomegaly, portal hypertension (ciliary dysfunction)
Cranioectodermal dysplasia	IFT122, WDR19, WDR35	Hepatic fibrosis (cholangiocyte ciliary dysfunction and abnormal ductal plate remodeling)
Glomerulocystic kidney disease	HNF1B	Increase in transaminase levels or, less frequently, cholestatic liver disease (impaired bile duct development)
Jeune chondrodysplasia	IFT80	Hepatic fibrosis (impaired ciliogenesis)
Joubert syndrome and related disorders	AHI1, ARL13B, CC2D2A, CEP290, NPHP1, RPGRIP1L, TMEM216, TMEM67	Hepatic fibrosis (cholangiocyte ciliary dysfunction)
KIF12 deficiency (PFIC type 8)	KIF12	Cholestasis (defective bile canalicular transport)
Mainzer-Saldino syndrome	IFT140	Cholestasis, hepatic fibrosis, hepatomegaly (ciliary dysfunction)
Meckel-Gruber syndrome	CEP290, CC2D2A MKS1, RPGRIP1L, TMEM67	Hepatic fibrosis (cholangiocyte ciliary dysfunction)
Nephronophthisis	NPHP1, INVS, NPHP3, NPHP4, NEK8, DCDC2	Hepatic fibrosis (cholangiocyte ciliary dysfunction)
Oral-facial-digital syndrome type I	OFD1	Liver cysts (abnormal biliary development)
Renal-hepatic-pancreatic dysplasia	NPHP3	Enlarged portal areas containing numerous elongated binary profiles with a tendency to perilobular fibrosis (cholangiocyte ciliary dysfunction)
ZFYVE19 deficiency (PFIC type 9)	ZFYVE19	Intrahepatic cholestasis, bile duct proliferation, hepatomegaly and fibrosis, cirrhosis (defective bile duct)
Alagille syndrome	JAG1, NOTCH2	Intrahepatic duct deficiency, cholestasis potentially progressive to cirrhosis (defective Notch signaling)	[30,31,32,33,34]

.

2.1. Ciliopathies

2.1.1. Ductal Plate Malformations

DPMs include congenital hepatic fibrosis (CHF), Caroli’s disease, Von Meyenburg complex (VMC), and polycystic liver disease (PCLD) [13]. CHF typically presents from the neonatal period to young adulthood. When CHF is associated with pre-existing bile duct dilation, it is referred to as Caroli’s syndrome, whereas congenital, non-obstructive saccular or fusiform dilatation of the large intrahepatic bile ducts alone defines Caroli’s disease [14]. It is also commonly observed that patients with DMPs can have congenital renal cysts or cystic kidney disease, which are considered part of the spectrum of hepatorenal ciliopathies.

The inheritance of CFH is generally recessive and, to date, only the PKHD1 gene has been clearly associated with the disease, with truncating variants generally producing more severe phenotypes than missense variants [15]. Notably, even individuals with the same mutation can show considerable variation in their liver and kidney involvement, suggesting modifying genetic or environmental factors. Recent studies show that high cyclic AMP levels in CHF can stabilize and activate β-catenin, enabling it to move to the nucleus and stimulate the expression of inflammatory chemokines. This process recruits macrophages and promotes fibrosis, creating a self-sustaining inflammatory environment. IL-1β signaling and inflammasome activation also contribute to this cycle [16].

2.1.2. Polycystic Liver Disease

PCLD is characterized by the progressive development and enlargement of cysts in the liver, which originate from the biliary epithelium [17], and typically shows autosomal dominant inheritance. Other organs such as the kidney or spleen may be involved with cyst formation with different degrees of severity [17]. Symptoms arise mainly from increasing liver size or cyst complications, causing abdominal pain, discomfort, and sometimes portal hypertension.

PCLD may be isolated or associated with autosomal dominant polycystic kidney disease (ADPKD). In the first case, the age of onset is generally in young adulthood and the main genes associated with PCLD are PRKCSH, SEC63, LRP5, ALG8, ALG9, GANAB, SEC61B, and DNAJB11 (Table 1) which encode proteins located mostly in the endoplasmic reticulum, where they play roles in proper folding and maturation of polycystin-1. Of note, PKD1 and PKD2, which encode the cilium-located proteins polycystin-1 and polycystin-2, are also associated with liver cysts, whose incidence gradually increases with age [18] and in young females, likely due to the effects of hormones on liver cysts [19].

In people with ADPKD-associated PCLD, every cell carries one germline mutation in the disease-related gene but, for a cyst to develop, a second somatic mutation on the other allele is needed, thus mimicking a recessive disease model while being inherited in a dominant pattern [20].

A key feature of cyst growth is altered intracellular signaling. Reduced polycystin activity leads to disrupted calcium regulation and increased cellular levels of cAMP. This shift stimulates protein kinase A and downstream pathways that promote cholangiocyte proliferation and fluid secretion, driving cyst enlargement [16].

Finally, an enrichment in single heterozygous PKHD1 mutations has been observed in patients with increased medullary echogenicity and multiple small liver cysts [21], thus suggesting the PKHD1 heterozygous carrier genotype as an autosomal dominant cause of PCLD, albeit with very low penetrance, and with cysts being typically small and in normal-sized livers [21,22]. Other studies also suggested that PKHD1 is an active gene essential for biliary homeostasis even in adulthood and that somatic mutations are the cause of disease presentation in heterozygous carriers [23].

2.1.3. Other Ciliopathies with Liver Involvement

Besides CHF and PCLD, other ciliopathies with multiorgan involvement may target the liver, impacting its functions to different degrees [24]. In general, ciliopathies often present with a wide range of clinical phenotypes, affecting multiple organs and falling under the definition of “syndromes”. The type and extent of liver involvement in these syndromes may vary significantly: hepatic fibrosis is a common finding in disorders such as nephronophthisis, Meckel–Gruber syndrome, Joubert syndrome, renal–hepatic–pancreatic dysplasia, Jeune chondrodysplasia, cranioectodermal dysplasia and COACH syndrome. In addition to fibrosis, disorders like Mainzer–Saldino syndrome, ZFYVE19 deficiency (commonly known as Progressive Familial Intrahepatic Cholestasis type 9, PFIC-9) and Bardet–Biedl syndrome can be characterized by cholestatic features. Other ciliopathies such as oral–facial–digital syndrome type I, glomerulocystic kidney disease and Alstrom syndrome may present with cysts, elevated transaminase levels and hepatomegaly with hepatic steatosis and chronic active hepatitis, respectively. Of note, it has been recently observed that KIF12 deficiency (PFIC type 8) might be included in this category, as its causative gene—KIF12—is regulated by HNF1β, which is known to be associated with bile duct morphogenesis defects and liver dysfunction [25].

Variants in other genes associated with cilia dysfunction, such as TTC26 or DCDC2, are associated with complex phenotypes presenting with hepatomegaly, neonatal cholestasis, ductal proliferation or neonatal sclerosing cholangitis that often leads to LT [26].

Finally, the PKD1L1 gene has been proposed as associated with syndromic forms of biliary atresia such as Biliary Atresia Splenic Malformation (BASM), whose genetic etiology remains unclear [27,28].

2.2. Alagille Syndrome

Alagille syndrome is an autosomal dominant disorder with multiorgan involvement caused by altered NOTCH signaling. The hallmark hepatic manifestation is early-onset cholestasis due to intrahepatic bile duct paucity, which presents with jaundice, pruritus, pale stools, hepatomegaly and splenomegaly. Malabsorption of fat-soluble vitamins often causes rickets and coagulopathy. Cardiac involvement typically includes pulmonary artery stenosis or other congenital heart defects, while skeletal abnormalities often include the classic “butterfly” vertebrae and distinctive facial features (broad forehead, deep-set eyes, pointed chin). Ophthalmologic findings (such as posterior embryotoxon) and renal/vascular malformations further contribute to the highly variable phenotype [30]. Genetically, Alagille syndrome is caused by mutations in either JAG1 (~95% of cases) or NOTCH2 (~5% cases) and phenotypic variability is a key feature, with the same variants possibly resulting in radically different presentations among affected individuals. The majority of JAG1 variants are protein-truncating mutations leading to haploinsufficiency as the main disease mechanism, while biallelic variants are presumed lethal [31]. Missense JAG1 mutations typically result in misfolded proteins retained intracellularly, unable to interact with the NOTCH2 receptor.

Some complex structural variants [32,33] as well as somatic variants or mosaicism have been reported as sources of phenotypic variability. Moreover, some authors suggest that some published evidence hints at modifier genes—such as POGLUT1, SOX9, THBS2, and PHB1 that modulate Notch signaling—as disease severity modulators, particularly in the liver [30].

On the other hand, most NOTCH2 variants are missense changes and the pathogenetic mechanisms remain less well defined [33]. Moreover, while NOTCH2-mutated patients show a significantly lower frequency of some of the classic extrahepatic features such as facial dysmorphisms, posterior embryotoxon, butterfly vertebrae and congenital cardiac defects, the rates of liver disease appear similar [34].

3. Diseases Caused by a Functional Impairment of the Liver

A wide range of diseases result from genetic defects affecting one or more hepatocyte functions. The severity of these conditions can vary significantly, not only between different disorders but also among individuals with the same diagnosis. In fact, some diseases can have little to no impact on liver morphology while profoundly disrupting specific secretive functions of the liver. Such disruptions can have widespread systemic effects and may frequently necessitate LT, as observed in certain inborn errors of metabolism.

To better classify such many different conditions, it can be useful to identify the function inside the hepatocyte that is prevalently impaired by the genetic variants.

3.1. Defects of Transporters or Transporter-Associated Molecules

This group of disorders is characterized by a dysfunctional surface membrane transporter in the liver or by a molecule implicated in its regulation or function [35]. Numerous disorders fall into this category, often with variable and distinct patterns of liver involvement through which we can subcategorize them (

Table 2. Representation of the most common genetic liver diseases caused by a defective transporter or transported-associated molecule. For each disorder, the associated genes and the degree of liver involvement are reported. Conditions marked with an asterisk have a minor impact on liver functionality but are still to be considered for differential diagnosis in specific cases. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Gene	Liver Involvement	Ref. N.
Dubin–Johnson syndrome	ABCC2	Asymptomatic or chronic idiopathic jaundice, persistent non-hemolytic hyperbilirubinemia without hepatocellular injury (impaired canalicular bilirubin excretion)	[36,37]
FIC1, BSEP and MDR3 deficiencies (PFIC/BRIC types 1, 2 and 3)	ABCB11, ABCB4, ATP8B1	Cholestatic jaundice and pruritus with normal serum levels of gamma-glutamyl transferase (GGT) in most cases. While BRIC is benign and with little to no evolution over time, PFIC can progress to liver fibrosis, cirrhosis and liver cancer (impaired bile acid transport)	[38,39,40]
Wilson’s disease	ATP7B	Hepatomegaly, liver failure, cirrhosis, increased risk of hepatocarcinoma (Hepatic copper accumulation)	[41,42,43]
Rotor syndrome	SLCO1B1, SLCO1B3	Conjugated hyperbilirubinemia (impaired hepatic uptake and storage of bilirubin)	[36,37]
NTCP deficiency	SLC10A1	Cholestasis and hepatomegaly with normal liver function (impaired bile acid uptake)	[44]
OST alpha/beta deficiency (PFIC type 6)	SLC51A, SLC51B	Cholestasis with portal fibrosis (defective bile acid transport)	[45]
Cystic fibrosis	CFTR	Biliary cirrhosis (abnormal chloride and bicarbonate secretion in bile ducts)	[46,47,48,49]
Niemann–Pick disease type C	NPC1, NPC2	Neonatal jaundice and hepatomegaly. Rarely can present with fatal acute liver failure (impaired intracellular lipid trafficking)	[50,51,52,53]
Fanconi–Bickel syndrome	SLC2A2	Hepatomegaly (impaired glucose transport)	[54]
Urea cycle defects (Citrin deficiency (citrullinemia type II), Hyperornithinemia–hyperammonemia–homocitrullinemia syndrome)	SLC25A13, SLC25A15	Hepatic steatosis and fibrosis. Sometimes can present with acute hepatitis (metabolic toxicity)	[55,56]
Carnitine deficiency (fatty acid oxidation defects)	SLC22A5	Hepatomegaly and steatosis (impaired mitochondrial fatty acid oxidation)	[57,58]
Infantile sialic acid storage disease *	SLC17A5	Hepatomegaly (lysosomal storage of sialic acid)	[59]
Cystinosis *	CTNS	Hepatomegaly, sclerotic cholangitis (lysosomal cystine accumulation)	[60]

). Of note, some of these disorders which affect canalicular transport proteins, such as ABCB11, ABCB4 and ATP8B1, impair bile acid export and destabilize hepatocyte polarity, leading to toxic bile accumulation, canalicular membrane injury, and progressive cholestasis. Because bile formation is most active in pericentral hepatocytes, injury often begins in this zone before spreading. The resulting damage extends beyond transport failure, triggering cytoskeletal collapse, bile leakage into the parenchyma, ductular reaction, and secondary fibrosis.

3.1.1. Defects of Bile Acid Transportation

Several conditions primarily affect bile acid transportation and therefore present with cholestasis as the dominant liver abnormality. These include FIC1 deficiency (PFIC type 1) and BSEP deficiency (PFIC type 2), which are caused by defects in canalicular membrane transporters, NTCP deficiency (SLC10A1) and OST α/β deficiency (SLC51A/SLC51B), both caused by defects in basolateral membrane transporters. In these disorders, impaired bile acid transport across canalicular or basolateral membranes leads to jaundice, pruritus, and, over time, varying degrees of fibrosis or progressive liver injury [35].

For FIC1 and BSEP deficiency, genotype–phenotype correlations have been described. FIC1 deficiency results from mutations in the ATP8B1 gene, which encodes the flippase FIC1 responsible for maintaining the phospholipid balance of the hepatocellular canalicular membrane. Truncating or null variants cause a complete loss of function, leading to severe, early-onset cholestatic disease and extrahepatic manifestations such as diarrhea and hearing loss. Milder missense mutations with residual activity can produce intermittent or benign recurrent cholestasis (BRIC1) [38]. A similar pattern is observed in BSEP deficiency which is caused by defects in ABCB11, encoding the bile salt export pump BSEP, which is the main canalicular transporter for bile acid secretion. In fact, null mutations cause early, rapidly progressive liver disease often complicated by hepatocellular carcinoma [39], whereas missense variants preserving partial function lead to milder phenotypes such as BRIC type 2, drug-induced cholestasis, or intrahepatic cholestasis of pregnancy [61]; heterozygous carriers may show transient cholestasis in response to hormonal or pharmacologic triggers [62] or adult-onset diseases like intrahepatic cholestasis of pregnancy [63]. Overall, null mutations across the two forms tend to produce severe, early-onset disease, whereas missense or heterozygous variants lead to milder, often intermittent cholestatic phenotypes.

Another disease in this category is NTCP deficiency, caused by mutations in the SLC10A1 gene, which encodes NTCP, the hepatocellular transporter responsible for bile acid uptake. Affected patients usually present with hypercholanemia, often accompanied by transient neonatal jaundice, and vitamin D deficiency during infancy, but all generally recover spontaneously with age, suggesting compensatory bile acid transport. The c.800C > T (p.Ser267Phe) variant seems very diffused in the population of affected individuals, suggesting a strong founder effect and potential evolutionary selection, as this variant also restricts hepatitis B virus entry into hepatocytes [44].

Finally, OST alpha/beta deficiency (PFIC type 6) is a rare disease with very few cases reported caused by mutations in the SLC51A and SLC51B genes which encode the OSTα-OSTβ complex, involving intestinal BA reabsorption in the enterohepatic circulation. Clinical presentation is characterized by jaundice and chronic malabsorptive diarrhea with high transaminases, γGT, and normal BA levels [45]. To date no significant genotype–phenotype correlations have been reported.

3.1.2. Defects of Phospholipid Transportation

MDR3 deficiency (PFIC type 3) stems from variants in ABCB4, which encodes the phospholipid transporter MDR3. Genotype–phenotype correlations like those observed in FIC1 and BSEP deficiencies apply to this disease as well. Also, disease severity correlates roughly with the degree of residual MDR3 activity, illustrating a near-linear relationship between genotype and clinical expression [40]. For MDR3 deficiency in particular, it has been observed that heterozygous carriers may show various phenotypes, particularly in adulthood, questioning the recessive inheritance model officially accepted to date [64].

3.1.3. Defects of Bilirubin Transportation

Finally, conditions such as Dubin–Johnson syndrome (ABCC2, encoding a canalicular membrane transporter) and Rotor syndrome (SLCO1B1/SLCO1B3, encoding basolateral membrane transporters) predominantly cause isolated hyperbilirubinemia without hepatocellular damage, reflecting defects in bilirubin handling rather than structural liver disease [36,37].

3.1.4. Defects of Copper Transportation (Wilson’s Disease)

Wilson’s disease (ATP7B) stands apart as a disorder of copper accumulation. Liver involvement is the first clinical manifestation in about 40–60% of patients, ranging from asymptomatic elevation of liver enzymes to cirrhosis, or acute liver failure [41]. Neurological and psychiatric symptoms such as movement disorders, dysarthria, gait disturbances, depression, personality changes, and psychosis are also common and can precede other findings. Characteristic ocular findings include the Kayser–Fleischer ring and, less commonly, sunflower cataracts. Other organ involvement may include renal tubular dysfunction, osteopenia, arthropathy, cardiomyopathy, endocrine and hematologic abnormalities. The disease is caused by mutations in the ATP7B gene, which encodes a transporter located in the trans-Golgi network and expressed in the liver and brain. Its primary function is to regulate copper homeostasis by mediating copper secretion into bile and plasma. More than 12,000 mutations have been identified so far, each leading to varying levels of residual protein activity, making genotype–phenotype correlations not always straightforward to establish [42,43]. Some geographical clusters have also been proposed: the missense variant H1069Q is the most frequent in European, North American and North African populations while R778L, C271* and M645R mutations appear more commonly in East Asian, Middle Eastern/South Asian and South American populations, respectively [43].

3.1.5. CFTR-Associated Liver Involvement

Finally, diseases like cystic fibrosis (CFTR) and Niemann–Pick disease (NPC1) may lead to biliary cirrhosis or severe neonatal liver dysfunction due to broader multisystem pathology involving bile ducts or lysosomal lipid processing.

Up to 30–40% of individuals with cystic fibrosis develop liver complications which contribute significantly to morbidity and mortality after pulmonary disease [46,47]. It typically manifests in childhood, with severe forms (multilobular cirrhosis and/or portal hypertension) developing in roughly 10% of patients by age 30 [47].

When CFTR is defective, stagnant, viscous bile irritates the biliary epithelium and favors obstruction and inflammation, which favor the development of biliary cirrhosis over time [46,47]. Moreover, CFTR deficiency disturbs biliary innate immunity, allowing Src tyrosine kinase and TLR4/NF-κB activation, which amplify inflammation [48]. Concurrent gut dysbiosis, intestinal inflammation, and endotoxin translocation exacerbate biliary injury through bile acid dysregulation and endotoxin-driven immune activation while endothelial dysfunction can trigger porto-sinusoidal vascular disease [49].

3.1.6. Other Disorders Associated with Deficits of Other Transporters

Niemann–Pick disease type C is caused by mutations in NPC1, which encodes a protein found on the limiting membrane of lysosomes, where it helps export cholesterol and certain lipids out of lysosomal storage. Occasionally, mutations affect NPC2, which encodes for a protein with similar function to NPC1 [50,51]. When NPC1 is defective, cholesterol and sphingolipids accumulate inside lysosomes, producing hepatomegaly and cholestasis. In infants, the overload can be brisk enough to produce acute liver failure while, over longer intervals, repeated cellular stress and immune activation can promote fibrosis [52]. Niemann–Pick disease shows a rather definite genotype–phenotype correlation, with truncating or loss-of-function alleles exhibiting the most rapid neurological progression [53] and missense mutations affecting phenotype based on topological categories—surface (SX, mild phenotype), partially buried (PBX, intermediate phenotype) and buried (BX, intermediate to severe phenotype) [50].

A subset of metabolic disorders primarily causes hepatomegaly and fat accumulation or fibrosis, reflecting systemic metabolic overload or storage.

Fanconi–Bickel syndrome is caused by mutations in SLC2A2, encoding the low-affinity facilitative transporter of glucose GLUT2, mainly expressed in renal tubular cells, enterocytes, pancreatic β-cells, hepatocytes and discrete regions of the brain. In hepatocytes, it is located in the basolateral (sinusoidal) plasma membrane and acts as a bidirectional transporter essential for glucose level homeostasis [54]. When GLUT2 is defective, the liver is involved as intracytoplasmic glycogen accumulation occurs, leading to hepatomegaly.

Carnitine deficiency is caused by mutation in the SLC22A5 gene, which encodes a plasma integral membrane transporter which functions both as an organic cation and as a sodium-dependent high-affinity carnitine transporter [57]. Carnitine is essential for the transfer of long-chain fatty acids from the cytoplasm into the mitochondria for beta-oxidation. Hepatic steatosis is determined by the resulting defective beta-oxidation of fats which, as a result, remain unused after release from adipose tissue and thus accumulate in the liver [58].

In citrine deficiency and hyperornithinemia–hyperammonemia–homocitrullinemia syndrome (SLC25A13 and SLC25A15 genes, respectively), the urea cycle is affected in an indirect or direct way, respectively. Specifically, citrin deficiency results in a broken aspartate supply and imbalanced cytosolic NADH/NAD+ ratio which results in steatosis and energy imbalance in hepatocytes, chronic stress, inflammation and fibrosis. Symptoms can be triggered or worsened by diet, especially high-carbohydrate meals, which increase NADH load and worsen metabolic imbalance [55]. On the other hand, SLC25A15 dysfunction results in a lack of effective ornithine transport inside the mitochondria, urea cycle block, hyperammonemia and metabolic stress, triggering liver steatosis and fibrosis [56].

Cystinosis is caused by mutations in the CTNS gene which encodes for a transporter that functions in cystine trafficking out of lysosomes. Defects in this process result in cystine accumulation inside lysosomes, crystal formation, cholangiocyte stress, and macrophage activation, triggering inflammation and fibrosis. Clinically, this can appear as hepatomegaly and sclerosing cholangitis-like disease [60].

3.2. Defects of Enzymes and Catalytic Molecules

This group of diseases includes several well-recognized hepatological disorders, such as Crigler–Najjar syndrome, Gilbert syndrome, and alpha-1 antitrypsin (A1AT) deficiency, as well as a broad range of metabolic conditions. These metabolic disorders result from defective enzymes that are primarily unable to perform their function in the liver but frequently have systemic effects, impacting the entire organism. Some disorders may be diagnosed incidentally as symptoms are negligible, while in some cases patients may present with liver damage or altered liver morphology (i.e., hepatomegaly or cholestasis) or even have severe systemic symptoms requiring emergency organ transplantation or the implementation of highly specific therapies [65]. A list of the disorders belonging to this group can be found in

Table 3. Schematic representation of the most common genetic liver diseases caused by a defective enzyme or catalytic molecule. For each disorder, the associated genes and the degree of liver involvement are reported. Conditions marked with an asterisk have a minor impact on liver functionality but are still to be considered for differential diagnosis in specific cases. A detailed list of gene symbols and associated name is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
Inborn error of bile acid synthesis	CYP7B1, AKR1D1, HSD3B7, CYP27A1, AMACR, HSD17B4, BAAT, SLC27A5, ACOX2, ABCD3, PEX10, PEX14, PEX19, PEX13, PEX6, PEX3, PEX1, PEX2, PEX16, PEX5, PEX12, PEX26, PEX7, PEX11B	Neonatal liver failure, neonatal cholestasis and CLD (impaired bile acid synthesis and accumulation of hepatotoxic intermediates)	[66,67,68,69,70,71,72,73,74,75,76,77]
Crigler–Najjar Syndrome	UGT1A1	Jaundice complicated by pruritus and progressive liver dysfunction (defective bilirubin conjugation)	[78,79,80,81]
Gilbert syndrome	UGT1A1	Asymptomatic, unconjugated hyperbilirubinemia and episodic jaundice (reduced bilirubin conjugation, typically triggered by fasting or stress)	[81,82,83]
Transaldolase deficiency	TALDO1	Hepatosplenomegaly with thrombocytopenia, hepatic dysfunction (toxic polyol accumulation)	[84,85]
AAT deficiency	SERPINA1	Hepatic fibrosis and cirrhosis (intracellular accumulation of misfolded alpha-1 antitrypsin)	[86]
Tyrosinemia type I	FAH	Hepatomegaly, acute liver failure, progression to cirrhosis (accumulation of toxic tyrosine metabolites)	[87,88,89,90]
Argininosuccinic aciduria	ASL	Hepatic fibrosis and hepatomegaly (ammonia toxicity and metabolic stress)	[87,91]
Citrullinemia, type I	ASS1	Hepatomegaly and cirrhosis in late-onset cases (urea cycle dysfunction)	[92,93]
Erythropoietic protoporphyria type I and X-linked	FECH, ALAS2	Gallstones and abnormal liver function possibly progressing to liver failure (hepatic protoporphyrin accumulation)	[94]
Lysosomal acid lipase deficiency	LIPA	Hepatomegaly with liver fibrosis possibly evolving into liver failure (lysosomal lipid accumulation)	[95,96]
Fatty acid oxidation defects	ACADM, HADHA, HADHB, ACADVL, ETFA, ETFB, ETFDH, GCDH, CPT1A, CPT2, SLC25A20	Hepatomegaly, steatosis and liver dysfunction ranging from mild to severe or Reye-like syndrome. Acute liver failure reported during pregnancy (impaired mitochondrial fatty acid oxidation)	[97,98,99,100]
S-adenosylhomocysteine hydrolase deficiency	AHCY	Hepatomegaly and cholestasis (impaired methylation and toxic metabolite accumulation)	[98]
Maple syrup urine disease *	DBT, PPM1K, BCKDHB, DLD, BCKDHA	The liver is not usually affected but, for these patients, transplantation is an option	[101]
Methylmalonic acidemia *	MMUT, MMAA, MMAB, MMADHC	Hepatomegaly (metabolic stress)	[101]
Propionic aciduria *	PCCB, PCCA	Hepatomegaly (metabolic stress)	[101]
Fructose intolerance *	ALDOB	Hepatomegaly, steatosis possibly evolving into cirrhosis (fructose-1-phosphate accumulation)	[102,103,104]
Glycogen storage diseases with liver involvement *	PGM1, AGL, GBE1, LDHA, SLC37A4, GYS2, PYGL, ALDOA, PHKG2, PHKB, G6PC, GAA, PHKA2	Hepatomegaly, fibrosis and steatosis, jaundice with chronic hepatitis (abnormal glycogen metabolism)	[105]
GM1 gangliosidosis *	GLB1	Hepatomegaly (lysosomal accumulation of gangliosides)	[106]
GM2 gangliosidoses *	HEXA, HEXB, GM2A	Hepatomegaly (lysosomal accumulation of gangliosides)	[107]
Gaucher disease *	GBA1	Hepatomegaly, steatosis (glucocerebroside accumulation)	[108]
Multiple sulfatase deficiency *	SUMF1	Hepatomegaly (lysosomal accumulation of sulfated substrates)	[109]
Alfa mannosidosis *	MAN2B1	Hepatomegaly (lysosomal accumulation of oligosaccharides)	[110]
Schindler disease *	NAGA	Hepatomegaly (glycoprotein accumulation)	[110]
Fucosidosis *	FUCA1	Hepatomegaly (lysosomal accumulation of fucose)	[110]
Sialuria *	GNE	Hepatomegaly (intracellular sialic acid accumulation)	[111]
Mucolipidosis 1–3	NEU1, GNPTAB	Hepatomegaly (lysosomal storage dysfunction)	[112,113,114,115]
Mucopolysaccharidosis type VI *	ARSB	Hepatomegaly (glycosaminoglycan accumulation)	[116]
PSK-α deficiency (PFIC type 13)	PSKH1	Putative association with cholestasis (impaired canalicular transport)	[117]
Galactosemia	GALE, GALM, GALT (GALK1)	Hepatomegaly, cholestasis, jaundice and cirrhosis in most severe cases associated with GALT (galactose metabolite toxicity)	[72]
Chronic Granulomatous Disease *	NCF1, NCF2, CYBA, CYBB, CYBC1, NCF4	Hepatomegaly, liver abscesses, and noncirrhotic portal hypertension (chronic inflammation)	[118]
Lathosterolosis *	SC5D	From asymptomatic elevation of liver enzymes to cirrhosis and liver failure needing transplantation (abnormal cholesterol biosynthesis)	[119]
Transient infantile hypertriglyceridemia and hepatosteatosis *	GPD1 (and CREB3L3 in mild forms)	Hepatomegaly, steatosis or fibrosis with abnormal liver enzymes and jaundice (impaired lipid metabolism)	[120]
Chanarin–Dorfman Syndrome *	ABHD5	Hepatomegaly, steatosis (defective triglyceride hydrolysis)	[121]
Shwachman–Diamond Syndrome *	SBDS, EFL1	Hepatomegaly (ribosomopathy)	[122]

along with the genes encoding the defective enzymes. A schematic view is reported in Table 3.

3.2.1. Alpha-1 Antitrypsin (AAT) Deficit

Hereditary alpha-1 antitrypsin deficiency is among the most prevalent monogenic conditions worldwide and is caused by pathogenic variants in SERPINA1, which encodes alpha-1 antitrypsin (AAT), a secreted serine protease inhibitor that protects hepatic and pulmonary tissues against unchecked proteolytic injury. AAT is synthesized predominantly in the liver hepatocytes, and disease-causing missense or splicing variants lead to polymerization and retention of misfolded AAT within the endoplasmic reticulum, promoting proteotoxic stress, hepatomegaly, elevated transaminases, and progressive liver injury. The most common severe variant, p.Glu342Lys (the Z allele), produces a marked reduction in circulating AAT levels when homozygous (ZZ genotype), conferring high risk for early-onset emphysema, chronic obstructive lung disease, and hepatic fibrosis or failure. The S allele, also frequent but less deleterious (p.Glu264Val), gives rise to moderate AAT reduction. Individuals with the wild-type M allele (MM genotype) maintain normal circulating AAT concentrations and liver structure. Although isolated heterozygosity (e.g., MZ genotype or MS) is typically insufficient to produce severe liver disease, carriers demonstrate increased vulnerability to hepatic injury under additional metabolic or inflammatory stressors, including NAFLD, alcohol exposure, or intercurrent hepatotoxic insults. Consequently, heterozygosity is recognized as a clinically relevant modifier that may amplify liver injury in the presence of other hepatic comorbidities, despite preserved baseline synthetic function [86].

3.2.2. Transaldolase Deficiency

Transaldolase deficiency is an autosomal recessive inborn error of metabolism caused by mutations that disrupt the activity of the TALDO1 gene product. TALDO1 encodes for a key enzyme in the non-oxidative side of the pentose phosphate pathway. When transaldolase is deficient, polyols and sugar phosphates accumulate in liver cells, leading to apoptosis, oxidative stress and ultimately hepatocellular damage, hepatomegaly, fibrosis, cirrhosis, or acute liver failure in infancy [84].

Liver disease is in fact the hallmark feature, present in over 85% of patients, followed by hematologic abnormalities such as anemia (75%) and thrombocytopenia (70%), tubulopathy and nephrolithiasis (30%), cardiac malformations and hypergonadotropic hypogonadism, delayed puberty, and rare thyroid abnormalities which occur in one third of the patients.

Biochemically, the accumulation of polyols and seven-carbon sugars in urine or plasma serves as a diagnostic biomarker. Enzyme assays confirm markedly reduced transaldolase activity (<6%), and genetic testing identifies biallelic TALDO1 variants, most frequently the c.793delC (p.Gln265Argfs*56) founder mutation in Middle Eastern families. No clear genotype–phenotype correlation has so far been established [85].

3.2.3. Crigler–Najjar Syndrome and Gilbert Syndrome

Crigler–Najjar syndrome and Gilbert syndrome are both caused by variants in the UGT1A1 gene, which encodes the hepatic enzyme uridine diphosphate–glucuronosyltransferase 1A1 responsible for bilirubin conjugation. The difference between these two entities relies on the degree of impairment of the enzymatic activity. Crigler–Najjar syndrome type I presents with a complete absence of functional enzyme activity due to null mutations, leading to severe unconjugated hyperbilirubinemia from the neonatal period, while in type II the phenotype is milder and is caused by partial impairment of enzymatic activity [78,79,80].

On the other hand, Gilbert syndrome is usually caused by mutations that leave 30–50% enzymatic UGT1A1 activity, resulting in mild, intermittent elevations of unconjugated bilirubin that become apparent during fasting, illness, or stress but are clinically benign and require no treatment. However, UGT1A1 activity can be relevant in pharmacological contexts (i.e., irinotecan in oncology [82,83]) in which UGT1A is implicated in drug metabolism. Among the most common variants associated with Gilbert syndrome worldwide is the promoter TATA box variant [A(TA)7TAA] that reduces transcription of the gene. However, numerous alleles have been described in association with the disease or with Crigler–Najjar syndrome and can be easily checked [81].

3.2.4. Inborn Errors of Bile Acid Synthesis

Inborn errors of bile acid synthesis are a complex group of diseases caused by defects in enzymes responsible for catalyzing key reactions in the synthesis of cholic and chenodeoxycholic acids or by secondary metabolic deficiencies like the Zelleweger spectrum disorders [66].

Among the genes responsible for primary defects are CYP7B1, AKR1D1, HSD3B7, CYP27A1, AMACR, HSD17B4, BAAT, SLC27A5, ACOX2, and ABCD3 which encode enzymes and transporters essential for bile acid synthesis and peroxisomal β-oxidation.

Some disorders have been better characterized than others in association with liver disease. Mutations in HSD3B7, which codes for 3β-hydroxysteroid-Δ⁵-C₂₇-steroid dehydrogenase, tend to cause neonatal cholestasis and fat-soluble vitamin malabsorption, conditions that usually improve with bile acid therapy [67,68]. Similarly, changes in AKR1D1 (also known as SRD5B1), the gene for Δ⁴-3-oxosteroid 5β-reductase, can lead to cholestatic liver disease and also interfere with steroid hormone metabolism [69]. Mutations in CYP7B1, encoding oxysterol 7α-hydroxylase, have been linked both to severe neonatal cholestasis and to hereditary spastic paraplegia type 5 (SPG5) in older individuals, with missense mutations being more frequently linked to the latter [70] and null mutations to the former [71]. Finally, two genes involved in bile acid conjugation—BAAT, which encodes bile acid-CoA:amino acid N-acyltransferase, and SLC27A5, which encodes bile acid-CoA ligase (FATP5)—can cause defects that prevent proper bile acid amidation, leading to disorders such as familial hypercholanemia [72,73].

Zellweger spectrum disorders are a group of autosomal recessive peroxisomal biogenesis disorders that lead to global defects in peroxisomal function, disrupting multiple metabolic pathways including bile acid synthesis, fatty acid oxidation, phospholipid formation, and glyoxylate detoxification. Clinically, patients may show neurologic abnormalities, developmental delay, seizures, hearing and vision impairment, adrenal insufficiency, enamel hypoplasia and liver dysfunction with hepatomegaly caused by the accumulation of C27-bile acid intermediates [74]. Genetically, Zelleweger spectrum disorders are caused by mutations in PEX1–PEX26 and related genes which encode peroxins, structural and regulatory proteins mediating peroxisome biogenesis, protein import, and organelle division required for peroxisome biogenesis and protein import [73,75].

For these disorders, genetic testing may be helpful to determine prognosis [76]. As an example, the common PEX1-p.G843D mutation is usually associated with a milder phenotype, while null mutations generally cause more severe cases [77]. However, for missense mutations or combinations of null and non-null mutations, the resulting phenotype is hard to predict, with many variables likely taking part in the determination of the outcome.

3.2.5. Aminoacidopathies: Tyrosinemia

Other metabolic diseases with relevant liver involvement are caused by mutations in FAH, ASL, and ASS1.

Tyrosinemia type I (hepatorenal tyrosinemia) is a severe autosomal recessive disorder of tyrosine metabolism caused by deficiency of the enzyme fumarylacetoacetase (encoded by the FAH gene), the final enzyme in the tyrosine degradation pathway. This defect leads to accumulation of toxic intermediates (fumarylacetoacetate, maleylacetoacetate, and succinylacetone) which damage the liver and kidneys [87].

Clinically, infants can present with acute liver failure before 6 months of age, showing jaundice, coagulopathy resistant to vitamin K, ascites, hypoglycemia, and hepatomegaly, often with a characteristic “boiled cabbage” odor. Chronic forms may present later with renal tubular dysfunction, rickets, or neurologic crises resembling acute intermittent porphyria (dystonia, neuropathy, respiratory failure). Untreated disease is typically fatal by age 2. A key element in tyrosinemia management is increased lifelong risk of hepatocarcinoma (HCC) which requires regular imaging and alpha-phetoprotein (AFP) monitoring [88,89,90].

Patients also require lifelong dietary restriction of tyrosine and phenylalanine to prevent secondary tyrosinemia and its complications (eye and skin lesions). LT is reserved for treatment failure or confirmed HCC [87].

3.2.6. Urea Cycle Disorders: Citrullinemia and Arginosuccinic Aciduria

In contrast, ASL (encoding argininosuccinate lyase and associated with arginosuccinic aciduria) and ASS1 (encoding for argininosuccinate synthase 1 and associated with citrullinemia) encode consecutive enzymes of the urea cycle. Deficiency of either enzyme leads to hyperammonemia and accumulation of argininosuccinate or citrulline which contribute to hepatic dysfunction and progression to CLD [87].

In the case of arginosuccinic aciduria, individuals with ≤8.7% enzyme activity have higher peak plasma ammonia levels, more frequently present with liver injury than those with greater activity. Cognitive outcomes also depended on enzyme activity: patients with enzymatic ≤ 24.3% activity showed significantly lower cognitive scores. Importantly, these thresholds mirror findings in citrullinemia type I, suggesting a shared biochemical behavior among distal urea cycle defects [91].

Citrullinemia shows similar pathogenic mechanisms, but some episodes of fulminant liver failure have also been reported as an initial presentation of the disease [92,93].

3.2.7. Fatty Acid Oxidation Defects

Another subset of diseases causing liver damage are fatty acid oxidation defects. The most common associated genes encode proteins involved in different steps of β-oxidation (Table 3). Overall, impaired β-oxidation limits the generation of acetyl-CoA, NADH, and FADH₂, leading to reduced ketone body synthesis and a deficiency of ATP during fasting or metabolic stress [97]. This energy crisis triggers hypoketotic hypoglycemia, the hallmark biochemical feature of these disorders. Accumulated fatty acyl-CoA intermediates and their derivatives (such as acylcarnitines and dicarboxylic acids) exert hepatotoxic effects, causing microvesicular steatosis, mitochondrial swelling, and hepatocellular necrosis. Over time, recurrent metabolic decompensations may lead to elevation of transaminases, hepatomegaly and progressive organ dysfunction [97].

S-adenosylhomocysteine hydrolase deficiency is a rare metabolic disorder with multiorgan involvement, caused by impaired methionine metabolism. The disease is primarily characterized by developmental delay, microcephaly, myopathy, hypotonia with markedly increased creatine kinase plasma levels, coagulation abnormalities and hepatopathy with cholestatic features which can in rare case progress to cirrhosis and hepatocarcinoma [98,99,100].

3.2.8. Galactosemia

Defects in galactose metabolism due to mutations in the GALT, GALE and GALK genes can lead to hepatomegaly, jaundice, anemia and intellectual disability, when galactosemia remains unrecognized and untreated. Phenotypes can be highly variable depending on the percentage of enzymatic activity left [i.e., loss-of-function (LOF) mutations vs. Duarte allele in GALT-associated galactosemia] which also reflects the different genetic variants found in patients. However, the liver is almost constantly involved, and most severe cases, often associated with GALT mutations, can also progress to cirrhosis [87].

3.2.9. Fructose Intolerance

Hereditary fructose intolerance involves a spectrum of hepatic phenotypes resulting from hepatocellular energy failure, chronic lipid accumulation, and impaired stress resilience. Acute liver involvement arises after fructose, sucrose, or sorbitol exposure, in which intracellular fructose-1-phosphate accumulation causes depletion of inorganic phosphate and ATP, inhibition of glycogenolysis and gluconeogenesis, and can precipitate fulminant infantile liver dysfunction, including severe neonatal acute liver failure with multiorgan involvement despite a normal newborn screen, particularly in patients homozygous for ALDOB c.448G > C (p.A150P), a variant which alone accounts for >50% of all alleles identified worldwide [102]. Subtle or partial-activity phenotypes manifest as hepatomegaly, isolated or intermittent hypertransaminasemia, or recurrent hepatitis-like episodes, leading to frequent misdiagnosis. Chronic exposure results in persistent macrovesicular steatosis, which may progress to steatohepatitis or fibrosis [103]. Hepatic tumors are rare, though isolated cases of hepatocellular adenomas with secondary inflammatory or granulomatous stress responses have been described [104].

3.2.10. Accumulation Disorders

Among the disorders falling in this category, the most relevant are lysosomal acid lipase (LAL) deficiency, mucolipidoses, sialidosis and Gaucher disease.

LAL deficiency is a metabolic disease caused by defects in the homonymous enzyme which breaks down cholesteryl esters and triglycerides into free cholesterol and fatty acids. When LAL activity is absent or severely reduced, lipids build up in multiple organs, particularly the liver, spleen, lymph nodes, bone marrow, and macrophages. This accumulation disrupts normal cellular and tissue functions, leading to progressive organ damage. The disorder is autosomal recessive and encompasses a spectrum of severity, with clinical features ranging from early-onset, rapidly fatal disease (Wolman disease) to milder, later-onset forms (cholesteryl ester storage disorder), depending on how much functional enzyme remains [95]. Liver is usually primarily involved, but diagnosis can be hard and a particularly mild form of the disease can be misdiagnosed as MASLD [96].

Mucolipidoses are diseases caused by the defective trafficking or processing of hydrolases within lysosomes which result in altered mannose-6-phosphate tagging of lysosomal enzymes which are thus misdirected to the extracellular space. This results in widespread accumulation of undegraded substrates within lysosomal compartments which also affects hepatocytes resulting in hepatomegaly [112].

Sialidosis is a specific mucolipidosis caused by mutations in the NEU1 gene. NEU1 variants are mostly missense mutations, causing variable enzyme instability, misfolding, and reduced catalytic activity, which explains the broad genotype–phenotype heterogeneity. However, as in many metabolic disorders, residual neuraminidase activity correlates with clinical severity. Moreover, some population-specific mutations have been described such as the c.544A > G (p.Ser182Gly) founder variant prevalent in Taiwanese patients [113,114].

On the other hand, mucolipidosis type II and III are more often associated with null mutations in the GNPTAB and GNTPG genes that abolish enzyme activity. Clinically, mucolipidosis type II presents at birth or prenatally with growth restriction, coarse facial features, skeletal dysplasia, joint stiffness, and severe progressive connective tissue abnormalities. Death typically occurs in early childhood.

Mucolipidosis type III tends to present with a milder, later-onset phenotype characterized by slow progression, joint contractures, hip disease, and relative preservation of cognition. Patients often survive until adulthood but with significant skeletal and mobility limitations. This has been proposed to be due to the common combination of hypomorphic mutations and a null variant [115].

Hepatic involvement in Gaucher disease results primarily from the accumulation of glucocerebroside-laden macrophages within the hepatic sinusoids. Progressive infiltration produces hepatomegaly and may contribute to portal hypertension and fibrosis. Although synthetic function is often preserved, advanced disease can lead to architectural distortion and, in rare cases, cirrhosis [108].

3.2.11. Glycogenoses with Liver Involvement

Glycogenoses—or glycogen storage diseases (GSDs)—are a wide group of diseases caused by defects in glycogen metabolism, but the patterns of liver involvement can vary widely depending on the specific enzyme affected. The subtypes of glycogenosis with major liver involvement are types 0, IV, VI, IX and XI. Manifestations range from mild fasting intolerance in GSD-0 to a wider phenotypic spectrum in GSD-IV, VI, IX, and XI that can present with intermediate liver involvement or more severe phenotypes such as progressive hepatic fibrosis or cirrhosis [105]. Tumorigenesis—particularly hepatic adenomas and hepatocellular carcinoma—occurs in types IV, VI, and IX, and rarely in XI [105].

3.2.12. Erythropoietic Protoporphyrias

Erythropoietic protoporphyria and X-linked protoporphyria arise from altered metabolic pathways driven by mutations in the FECH and ALAS2 genes, respectively. In this case, impaired heme metabolism leads to the accumulation of protoporphyrin IX in erythrocytes and its release in the circulation where photoexposure charges it positively, inducing energy transfer to oxygen and generation of tissue-damaging reactive oxygen species (ROS). Clinically, the main manifestation is phototoxic reactions characterized by severe pain, although the skin typically exhibits no visible alterations at least within the first hours after exposure. Among protoporphyrias complications, cholestatic liver disease and liver failure are the most severe [94].

3.3. Defects of Signaling Molecules or Receptors

In this subclass of disorders, genetic variants affect proteins involved in cellular signaling pathways. The most frequently diagnosed conditions are hemochromatosis [123], FXR deficiency (PFIC type 5) [124], familial hypercholesterolemia [65], hepatorenocardiac degenerative fibrosis [125], partial lipodystrophy [126] and non-syndromic portal hypertension [127]. These diseases exhibit a broad spectrum of clinical presentations and degrees of liver involvement. In particularly severe cases, LT may be required, as detailed in

Table 4. Schematic representation of the most common genetic liver diseases caused by a defective receptor or signaling molecule. For each disorder, the associated genes and the degree of liver involvement are reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
Hemochromatosis	HFE, HFE2, HAMP, TFR2, SLC40A1	Elevated transaminase, CLD possibly leading to cirrhosis and increased risk of HCC (hepatic iron overload)	[123,128,129,130,131,132,133,134,135,136,137]
FXR deficiency (PFIC type 5)	FXR (NR1H4)	Hepatic fibrosis with ductal reaction, diffuse giant cell transformation, ballooning hepatocytes and progression to cirrhosis (impaired bile acid homeostasis)	[124,138,139]
Progressive Familial Intrahepatic Cholestasis type 11	SEMA7A	Cholestasis, jaundice, with normal GGT, elevated serum transaminases and bile acids (impaired hepatobiliary signaling)	[140]
Hepatorenocardiac degenerative fibrosis	TULP3	Liver fibrosis (defective primary cilium-dependent signaling)	[125]
Lipodystrophy, familial partial, type 3	PPARG	Liver steatosis and cirrhosis (severe insulin resistance and altered lipid metabolism)	[126]
Noncirrhotic portal hypertension type 2	GIMAP5	Hepatomegaly with portal hypertension (vascular and immune-mediated liver injury)	[127,141]

.

3.3.1. Iron Accumulation Disorders

Hemochromatosis is a genetic disorder caused by iron accumulation in multiple organs due to excessive intestinal iron absorption and dysfunctional homeostasis regulation. The disease is more prevalent in Northern Europe, while a lower incidence is observed in people of African descent. From a genetic point of view, the most common form is type 1, associated with mutations in HFE, in which some disease-causing polymorphisms have been identified and characterized across multiple populations. The most frequent polymorphism is C282Y, which has an allelic frequency in the global population of 6.2% [128]. Among C282Y homozygotes, biochemical penetrance (i.e., elevated transferrin saturation or ferritin) may be ~75% in men and ~50% in women, but clinical penetrance (iron-related organ damage) is much lower [129]. Another genetic variant frequently found in the general population is the H63D mutation. However, its clinical impact is nowadays considered limited and individuals who are compound heterozygotes (C282Y/H63D) or heterozygotes for H63D generally have much lower risk of clinically significant iron overload. Individuals carrying H63D without C282Y should therefore not be considered at increased risk of iron overload [130]. It is important to highlight that genotype–phenotype correlations are not easy and genotype alone is not sufficient to predict the phenotype, which appears to be influenced by modifiers such as gender [131], alcohol intake [132] and co-morbid liver disease (e.g., MASLD, hepatitis C) [133]. Rarer but more severe forms of hemochromatosis have also been associated with mutations in hemojuvelin (HFE2, hemochromatosis type 2A), hepcidin (HAMP, hemochromatosis type 2B), transferrin receptor 2 (TFR2, hemochromatosis type 3), and ferroportin (SLC40A1, hemochromatosis type 4). Mutations in hemojuvelin have shown population-specific distributions: G320V and L101P appear to be confined to Caucasians, Q6H and C321* seem predominant in Chinese patients, while I281T, A310G, and R385* were reported in multiple ethnic groups [134]. Moreover, missense mutations more often lead to hypogonadism than nonsense mutations [134]. Other subsets of hemochromatosis derive from mutations in hepcidin or in molecules implicated in its production and function such as TFR2 with both missense and nonsense mutations being scattered along the whole gene [135]. Also, in HAMP-associated hemochromatosis, hypogonadism is a frequent complication [136]. All forms of hemochromatosis described so far have an autosomal recessive inheritance pattern except for type 4 (also known as ferroportin disease) which is inherited in an autosomal dominant pattern. SLC40A1 variants are mostly missense mutations with very few LOF mutations reported which cause impaired iron export and macrophage iron loading with high ferritin but normal or low transferrin saturation. Gain-of-function mutations (often referred to as hepcidin-resistant), on the other hand, lead to excessive iron release, high transferrin saturation, and hepatocellular iron overload resembling classic hemochromatosis. These mutations are typically clustered in transmembrane or hepcidin-binding domains and produce a broad clinical spectrum with variable liver involvement depending on the functional impact of the specific variant [137].

3.3.2. FXR Deficiency (PFIC Type 5)

FXR deficiency (PFIC type 5) is a rare, very rapidly progressive form of PFIC characterized by early-onset coagulopathy, normal GGT activity and elevated AFP levels caused by mutations in NR1H4, which encodes for a nuclear receptor and transcription factor (FXR) that naturally binds bile acids and regulates their homeostasis, ensuring a balance between uptake, synthesis and export [138]. Only a few cases have been described so far, mainly associated with LOF mutations [139].

3.3.3. Semaphorin-7A Deficiency (PFIC Type 11)

Semaphorin-7A deficiency (PFIC type 11) is caused by mutations in the SEMA7A gene, which encodes the membrane-associated signaling protein Semaphorin-7A. These variants likely exert a gain-of-function effect, leading to downregulation of key bile canalicular transporters such as BSEP and MRP2 in hepatocytes, thus resulting in cholestasis, jaundice, normal GGT levels, and elevated serum transaminases and bile acids [140].

3.3.4. Hepatorenocardiac Degenerative Fibrosis

Another recently characterized disorder is associated with the TULP3 gene, which encodes an adaptor protein with a critical role in ciliary trafficking of integral membrane proteins.

The disorder is usually characterized by cholestatic liver enzymes, fibrosis, cirrhosis with bridging portal fibrosis with minimal inflammation and ductular reaction, and eventually portal hypertension. The kidney and heart can also be involved as chronic kidney disease with hyperechogenic kidneys, tubular dilatation, interstitial fibrosis, and hypertrophic non-obstructive cardiomyopathy with myocardial fibrosis [125].

3.3.5. Lipodystrophy, Familial Partial, Type 3

Familial partial lipodystrophy type 3 results from loss-of-function variants in the PPARG gene, which encodes the transcription factor peroxisome proliferator-activated receptor gamma (PPARγ), a master regulator of adipogenesis, lipid storage, and insulin sensitivity. This leads to impaired adipocyte differentiation and function with accumulation of triglycerides and free fatty acids in hepatocytes, causing steatosis [126].

3.3.6. Noncirrhotic Portal Hypertension Type 2

Finally, porto-sinusoidal vascular disorder can also result in portal hypertension without the presence of liver cirrhosis. Among these disorders, noncirrhotic portal hypertension type 2 is one of the better characterized and results from impaired function of the GTPase encoded by the GIMAP5 gene [127,141].

3.4. Defects of Intracellular Trafficking

3.4.1. ARC and MYO5B Deficiency

The most relevant conditions in this group are ARC syndrome (PFIC type 10) and MYO5B deficiency (PFIC type 12). In this disease group, the main dysfunction occurs in proteins that take part in the intracellular trafficking of molecules between the membrane and the other cellular compartments of the hepatocyte. The phenotype is variable but is usually characterized by cholestasis with different degrees of severity and progression [142].

ARC syndrome, or its milder phenotype PFIC type 12, is caused by dysfunction of the VPS33B gene, which encodes a protein involved in membrane trafficking that interacts with RAB11A at recycling endosomes and is crucial for hepatocyte polarity [143]. In its classical form, ARC syndrome is characterized by dysmorphic features, heart malformations, cholestasis, kidney dysfunction, neurologic impairment and other syndromic features present at different incidences and severities in different subjects. ARC syndrome is usually associated with LOF mutations. On the other hand, missense variants can cause a milder form of diseases with mainly liver involvement classified as PFIC type 12 [144].

A similar spectrum of symptoms is reported for MYO5B deficiency, which is caused by mutations in MYO5B, a gene typically associated with microvilli inclusion disease but recently described also in association with cholestasis. From a molecular point of view, MYO5B interacts with rab11a, thus granting the correct trafficking and localization of BSEP on the hepatocyte plasma membrane [145].

3.4.2. Other Disorders

Other complex monogenic disorders can be classified within this category, as the causative genes encode for proteins involved in intracellular trafficking. However, liver involvement is usually secondary or occurs after primary signs and symptoms have already allowed a clinical or molecular diagnosis. The most notable disorders are infantile liver failure syndrome types 2 and 3 and spinocerebellar ataxia, autosomal recessive type 21, associated with the NBAS, RINT1 and SCYL1 genes, respectively. Hepatic involvement typically includes abrupt elevations in transaminases, coagulopathy, and varying degrees of cholestasis, with rapid onset during metabolic stress. Between episodes, liver function may normalize, although some patients develop chronic hepatic injury [146,147,148].

A schematic view of this group of disorders, along with the associated genes and liver phenotypes, is reported in

Table 5. Schematic representation of the most common genetic liver diseases caused by a defective molecule involved in intracellular trafficking. For each disorder, the associated genes and the degree of liver involvement are reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
ARC syndrome (PFIC type 12)	VPS33B	Mild cholestasis with hepatomegaly and giant cell formation (defective intracellular vesicular trafficking)	[142,143,144]
MYO5B deficiency (PFIC type 10)	MYO5B	Hepatomegaly, cholestasis, fibrosis and giant cell formation (impaired apical membrane trafficking)	[145]
Arthrogryposis, renal dysfunction, and cholestasis 2	VIPAS39	Cholestasis with bile duct paucity, giant cell hepatitis, pigmentary deposits and portal tract fibrosis (defective vesicle trafficking)	[149]
Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis	VPS50	Neonatal cholestasis with rosetting of hepatocytes and disrupted bile-canaliculus tight junctions (defective vesicle trafficking)	[150]
Hemophagocytic lymphohistiocytosis, familial, 5, with or without microvillus inclusion disease	STXBP2	Hepatomegaly, liver dysfunction possibly evolving to liver failure (immune-mediated liver injury and impaired vesicle exocytosis)	[151]
Osteootohepatoenteric syndrome	UNC45A	Neonatal onset jaundice, severe cholestasis, microvesicular steatosis, liver fibrosis (defective protein trafficking)	[152]
MEDNIK syndrome	AP1S1	Hepatic fibrosis, hepatomegaly, cholestasis, and cirrhosis (impaired intracellular protein trafficking)	[153]
Keratitis-ichthyosis-deafness syndrome	AP1B1	Hepatomegaly and liver dysfunction (defective vesicular transport and epithelial polarity)	[153]
Infantile liver failure syndrome 2	NBAS	Acute episodic liver failure (impaired intracellular protein trafficking and ER stress)	[146,147,148]
Infantile liver failure syndrome 3	RINT1	Acute episodic liver failure with hepatomegaly, steatosis and focal cholestasis (defective ER–Golgi trafficking)
Spinocerebellar ataxia, autosomal recessive 21	SCYL1	Acute episodic liver failure with hepatomegaly, steatosis and focal cholestasis (defective ER–Golgi trafficking)

.

3.5. Defects in Cell–Cell Junction Formation

This group of diseases includes three disorders, TJP2 deficiency (PFIC type 4), USP53 deficiency (PFIC type 5) and neonatal ichthyosis-sclerosing cholangitis (NISCH) syndrome, whose pathological mechanisms are not yet fully understood. These conditions are extremely rare, with fewer than 10 reported cases of NISCH syndrome to date. These disorders are caused by pathogenic variants in genes encoding proteins located and involved in the formation of cell junctions (

Table 6. Schematic representation of the most common genetic liver diseases caused by a defective molecule involved in the formation of cellular junctions. For each disorder, the associated genes and the degree of liver involvement are reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
TJP2 deficiency (PFIC type 4)	TJP2	Intrahepatic cholestasis, increased bilirubin and bile acids, and portal hypertension (defective tight junction integrity in hepatocytes)	[72,138]
USP53 deficiency (PFIC type 7)	USP53	Cholestasis (impaired tight junction function and disrupted bile canalicular integrity)	[154]
NISCH syndrome	CLDN1	Hepatomegaly, cholestasis and fibrosis, sclerosing cholangitis with progression to CLD and portal hypertension (defective tight junction-mediated bile duct barrier function)	[155]

). Patients typically present with cholestasis and liver dysfunction.

TJP2 deficiency is clinically characterized by childhood onset, rapidly progressing cholestasis with normal or mildly increased serum GGT [138]. Histologically elongated tight junctions between adjacent hepatocytes and biliary canaliculi are often seen on biopsy. Genetically it is usually associated with LOF mutations while missense mutations have been linked to familial hypercholanemia type 1. This disorder is characterized by markedly increased serum levels of conjugated bile acids, causing intense pruritus, fat malabsorption, and failure to thrive. The impaired absorption of dietary fats leads to deficiencies of fat-soluble vitamins [72].

USP53 deficiency results from variants in USP53, a protein contributing to tight junction formation. The disease often presents with low γ-glutamyltransferase (GGT) cholestasis, elevated serum bile acids and modestly elevated aminotransferases occurring episodically and in a self-limiting behavior [154].

In the case of NISCH syndrome, additional features such as sclerosing cholangitis, skin scaling, hypotrichosis, alopecia, hypodontia or oligodontia, and enamel dysplasia can aid in diagnosis [155].

3.6. Defects Affecting Mitochondrial Functions

This group encompasses conditions arising from different pathological mechanisms impacting mitochondrial functionality. Each class of diseases has a specific underlying pathological mechanism usually related to the maintenance of mtDNA, defects of the mitochondrial respiratory chain and loss or rearrangement of mtDNA [156].

3.6.1. Mitochondrial DNA Depletion Syndromes

Mitochondrial DNA depletion syndromes are severe, early-onset disorders caused by defects in nuclear genes required for the maintenance and replication of mitochondrial DNA, such as MRM2, TFAM, TWNK, POLG, MPV17, TRMU, DGUOK, TK2 and TYMP. Hepatic mtDNA content is usually reduced to 1–20% of normal, resulting in decreased activity of mitochondrial respiratory chain complexes and consequent energy failure. Affected neonates generally present within the first months of life with failure to thrive, poor growth, vomiting, and jaundice, progressing to hepatic failure with hepatomegaly, cholestasis, steatosis, micronodular cirrhosis, hepatocellular necrosis, periportal fibrosis, and pseudo-acinar formation. Neurologically, patients develop encephalopathy, hypotonia, seizures, hyperreflexia, cerebral atrophy, and peripheral neuropathy. Laboratory findings show elevated bilirubin and transaminases, hypoalbuminemia, lactic acidosis, hypoglycemia, and generalized aminoaciduria [156,157]. The disease course is usually acute, with hepatic failure typically developing in the first months of life. Mortality is high, even in patients who undergo LT [157,158].

Genetically, the most common forms are associated with POLG, DGUOK, TK2 and MPV17 mutations [159]. Of note, MPV17-associated mitochondriopathy is also known as Navajo neurohepatopathy as it is speculated that it originated in the reservations of the Southwest of USA thanks to a founder effect (c.149G > A, R50Q mutation) [160].

3.6.2. Respiratory Complex Deficiencies

Defects in molecules responsible for the functioning of the respiratory complex (I to IV) result in severe mitochondrial disorders with liver involvement. The better characterized are those associated with the SCO1 and BCS1L genes, which encode for a mitochondrial membrane copper chaperone for complex IV and a protein involved in the assembly of respiratory complex III, respectively [161,162]. Clinical presentation is usually dominated by severe and often lethal neurologic disorders (hypotonia, encephalopathy and delayed psychomotor development) and metabolic acidosis, hypoglycemia and failure to thrive. The liver can be involved at different levels, with cholestasis, steatosis and fibrosis being the most common occurrences [163].

3.6.3. Pearson Marrow Pancreas Syndrome

Pearson syndrome is a mitochondrial disorder caused by large-scale deletions of mitochondrial DNA, classically presenting in infancy with bone marrow failure and pancreatic insufficiency. Liver involvement is prominent and includes marked hepatomegaly, steatosis, fibrosis, and progression to cirrhosis, sometimes leading to hepatic failure and death before 4 years of age. Histologically, the liver shows fatty infiltration and mitochondrial structural abnormalities reflecting systemic oxidative phosphorylation failure [164,165].

3.6.4. Villous Atrophy with Hepatic Involvement

Villous Atrophy Syndrome, another mitochondrial disease with multisystem features, manifests in infancy with vomiting, diarrhea, and intestinal villous atrophy. Hepatic involvement is milder than in Pearson syndrome, presenting as hepatomegaly, steatosis, and mild elevation of aminotransferases. Despite transient improvement of gastrointestinal symptoms, the disease eventually progresses to multisystem failure. In both conditions, hepatic steatosis and mitochondrial dysfunction are key pathological features reflecting the underlying impairment of energy metabolism [164].

Detailed information on liver involvement is reported in

Table 7. Schematic representation of the most common genetic liver diseases caused by a defect in mitochondrial functions. For each disorder, the associated genes and the degree of liver involvement are reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
Mitochondrial DNA depletion syndrome	MRM2, TFAM, TWNK, POLG, MPV17, TRMU, DGUOK, TK2, TYMP	Hepatomegaly, steatosis, fibrosis with decreased liver function often leading to fatal hepatic failure (mitochondrial DNA depletion)	[156,157,158,159,160]
Respiratory complex deficiencies	ACAD9, BCS1L, SCO1	Hepatomegaly, steatosis, fibrosis, cholestasis and cholangitis, with decreased liver function possibly leading to liver failure (mitochondrial respiratory chain dysfunction)	[161,162,163]
Pearson marrow pancreas syndrome	mtDNA deletions	Liver steatosis and dysfunction (mitochondrial DNA depletion)	[164,165]
Villous atrophy with hepatic involvement	mtDNA rearrangements	Mild elevation of liver enzymes, steatosis, hepatomegaly (mitochondrial DNA dysfunction)	[164]

. Due to the systemic nature of the diseases, there is no consensus on the utility of LT and outcomes are often unsatisfactory [164].

3.7. Genetic Disorders with Lesser Evidence of Liver Involvement

Genetic diseases can affect the liver to varying degrees of severity, altering its anatomy and functionality in different ways. However, liver involvement in some genetic disorders is minimal, or the evidence linking these disorders to liver damage is limited and based on anecdotal cases reported in the literature. Additionally, certain conditions, such as MASLD, are complex disorders in which genetic contributions represent just one of several factors influencing the phenotype. In such cases, the genetic contribution is most often considered polygenic.

All conditions within this category have been classified using the same criteria as above and are summarized in

Table 8. Schematic representation of genetic liver diseases for which the association with liver disease is not strong and clinical manifestations are diverse. For each disorder, the class under which it falls, the associated genes and the degree of liver involvement are reported. When appropriate, a reference to the available published data showing the association of the disease with liver conditions has been reported. A detailed list of gene symbols and associated names is available in Supplementary Table S1.

Disease Name	Associated Genes	Liver Involvement	Ref. N.
Anatomical Defects
Ellis–Van Creveld syndrome	EVC, EVC2	Paucity/dysplasia of bile ducts and cirrhosis, liver hemangioma (abnormal ciliogenesis)	[164,165,166]
Senior Løken syndrome	NPHP1, INVS, NPHP3, NPHP4, IQCB1, CEP290, SDCCAG8, WDR19, CEP164 e TRAF3IP1	Hepatic fibrosis (biliary development defects)	[24]
Transporter Defects
Zimmermann–Laband syndrome 3	KCNN3	Hepatomegaly, non-cirrhotic portal hypertension (altered cellular ion transport)	[155]
ABCC12 deficiency	ABCC12	Idiopathic chronic cholestasis (impaired transporter-mediated biliary excretion)	[167]
Sitosterolemia	ABCG5, ABCG8	Reported cases of cirrhosis. Can be treated with LT (sterol accumulation)	[168]
Defects of Enzymes and Catalytic Molecules
Acute intermittent porphyria	HMBS	Increased risk of HCC (chronic hepatic porphyrin accumulation)	[169]
Aspartylglucosaminuria	AGA	Hepatomegaly (lysosomal accumulation of glycoprotein degradation products)	[170]
Mucopolysaccharidoses	GLB1, HYAL1, IDUA, ARSB, ARSK, GUSB, HGSNAT, GALNS, NAGLU, SGSH, IDS	Hepatomegaly (lysosomal glycosaminoglycan accumulation)	[116]
Galactosialidosis	CTSA	Hepatomegaly (lysosomal accumulation of sialylated compounds)	[110]
Smith–Lemli–Opitz syndrome	DHCR7	Cholestatic liver disease (impaired cholesterol biosynthesis)	[171]
Peripheral neuropathy with variable spasticity, exercise intolerance, and developmental delay	TRMT5	Cirrhosis, portal hypertension (impaired mitochondrial function)	[172,173]
Abetalipoproteinemia	MTTP	Steatosis (in some patients) (impaired lipoprotein assembly)	[174]
Signaling Molecules/Receptor Defects
Infantile Intrahepatic Cholestasis	LSR	Intrahepatic cholestasis (impaired bile acid transport)	[175]
Polygenic Disorders
MASLD	PNPLA3, GCKR, TM6SF2, MBOAT7, GPAM, HSD17B13, PPP1R3B, CYP8B1	Genes with putative effect on the phenotype of MASLD patients (polygenic variants affecting hepatic lipid metabolism)	[176,177]

for easier reference. The relevant literature describing the liver involvement in these conditions is also included in the table.

4. Why a Genetic Diagnosis?

Genetic testing has become an indispensable tool in the diagnosis and management of inherited liver diseases. While traditional methods like liver biopsies, blood tests, and imaging can identify physical or biochemical abnormalities, they often fall short in defining a specific diagnosis or pinpointing the causative genetic mutation. Sequencing approaches, from targeted panels to whole-exome and whole-genome sequencing, provide a molecular definition of disease, enabling precise differentiation among disorders with overlapping clinical or biochemical profiles (e.g., cholestatic disorders) [35]. Genetic testing also offers a key benefit by refining genotype–phenotype correlations through the identification of specific mutation types. This capability can provide prognostic insight into disease severity, age of onset, and likelihood of extrahepatic involvement. A relevant example is metabolic disorders, where specific variants differentially impact residual enzymatic activity, thereby explaining the wide range of clinical manifestations observed (vide infra). In many cases, genetic testing also guides therapy. For example, the identification of POLG mutations prevents the use of valproate [178], UGT1A1-specific mutations inform on irinotecan dosage and usability [82,83] or responsiveness to phenobarbital [179], and variant characterization in transporter defects can guide the use of targeted therapies such as maralixibat or odevixibat [180]. Beyond the individual, genetic diagnosis supports family counseling, carrier detection, and reproductive planning, which are particularly relevant in recessive or geographically clustered disorders.

A broad range of methodologies for genetic testing is currently available, ranging from targeted single-gene tests and small gene panels to whole-genome sequencing. While single-gene testing is nowadays less common due to its limitations in versatility and a low efficacy–expense rate, gene panels are still used in a diagnostic setting, particularly for disorders with highly specific clinical features (e.g., alpha-1 antitrypsin deficiency or Wilson disease). In fact, these approaches offer rapid turnaround times, straightforward interpretation, and relatively low cost. However, the risk of underdiagnosis when phenocopies are present and the need for additional tests bring up the prices and limit applicability.

Larger next-generation sequencing (NGS) panels, such as clinical exome or whole exome, provide a more comprehensive option with good scalability, declining per-gene cost, and broad availability across diagnostic laboratories. The application of these tests increases the diagnostic yield, particularly in heterogeneous conditions (e.g., cholestasis, cryptogenic cirrhosis) and allows for data re-analysis and over-time re-evaluation. However, a higher burden of variants of uncertain significance (VUS) is usually observed, whose interpretation remains critical, and the lack of coverage in intronic regions as well as copy number alteration calls represents major limitations [181].

For this reason, whole-genome sequencing (WGS) is increasingly emerging as the most suitable near-future option even in clinical practice as it offers full coverage over the whole genome and allows easier detection of structural variants [182]. Moreover, its costs have decreased substantially over recent years, and issues of machine availability are becoming progressively easier to overcome due to growing commercial competition among sequencing providers [183]. The main downsides that persist are the lack of bioinformatic infrastructure, longer analysis time, and experienced multidisciplinary teams for variant interpretation [184]. Also, availability and reimbursability represent an issue, as they vary greatly by country and healthcare system, with some national programs now routinely funding whole-exome sequencing (WES) or WGS for rare diseases and others restricting reimbursement to more basic and limited approaches [185].

Overall, the adoption of the broadest feasible testing strategy is recommended whenever possible as it maximizes diagnostic yield, reduces the need for sequential testing, and facilitates early diagnosis [181]. Indeed, a widespread molecular characterization also strengthens disease classification, allowing a transition from descriptive phenotypes to mechanistically defined entities, which better reflect the complex biological diversity of diseases.

5. Next Steps: Multi-Omics and Data Sharing

Despite remarkable advances, many genetic liver diseases remain only partially understood, and a significant fraction of patients still lack a molecular diagnosis. The diagnostic rate of genetic testing is in fact variable depending on the specific test, the disease and the age group. In children, metabolic disorders can reach a 55% [186] diagnostic yield while a generic liver phenotype only reaches a ~20% diagnostic rate [6]. The same applies to an adult population, in which clinical presentations can be more subtle and harder to characterize [187].

To further study unsolved cases and uncover new disease mechanisms, multi-omics approaches have emerged as tools capable of reshaping our understanding of disease by integrating different branches of molecular biology such as epigenetic regulation, transcriptional processes, proteomic remodeling, and metabolic fluxes across disease stages [188]. This integrative perspective is particularly powerful in liver diseases where heterogeneous genetic background and dynamic microenvironmental cues drive progression [189].

Among these conditions, one of the most studied is MASLD, where metabolomics, lipidomics, transcriptomics, and microbiome profiling have been used to distinguish disease stages, predict fibrosis progression, and identify non-invasive biomarkers [190,191]. However, other disease models have been extensively studied such as cirrhosis [192], ALD [193], HCC [194] and cholangitis [195]. This has been made easier by the advent of artificial intelligence which has made the analysis of multidimensional biological datasets faster and more accessible [196].

In parallel, liver organoid systems derived from primary tissue or pluripotent stem cells and coupled with CRISPR-based modeling have emerged as a tractable experimental platform to functionally validate candidate mechanisms identified through multi-omics profiling [197,198].

Crucially, the impact of these approaches is amplified by robust data-sharing frameworks and open-access resources, which allow independent validation, cross-cohort comparisons, and meta-analytic integration across studies. Publicly available multi-omics repositories and harmonized data standards facilitate reproducibility and enable the re-analysis of datasets [199].

On the therapeutic front, the field is moving toward precision interventions, including enzyme replacement, small-molecule modulators, and gene therapy [200,201], but equitable access to these therapies and procedures as well as to genetic testing and counseling is a global need which still remains only partially addressed.

6. Conclusions

Genetic liver diseases are a highly heterogeneous and complex group of disorders, characterized by diverse etiological mechanisms, variable penetrance, overlapping phenotypes, and a broad clinical spectrum. In this review, by matching each disorder with its underlying mechanism, we aim to help clinicians navigate an increasingly complex genetic landscape, guiding both diagnostic reasoning and the interpretation of sequencing results. This approach also offers a common language for researchers, enabling clearer hypothesis generation and cross-disease comparisons, ultimately supporting more precise and personalized strategies in hepatology.