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Functional Genomics of Rare Variants in Human Disease

A Special Issue of International Journal of Molecular Sciences (ISSN 1422-0067) belonging to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 614

Editor

Special Issue Information

Dear Colleagues,

The rapid implementation of next-generation sequencing technologies has led to an unprecedented expansion in the identification of rare genetic variants across the human genome. While these variants are increasingly detected in both research and clinical settings, their functional interpretation remains a major challenge, particularly in the context of complex and heterogeneous human diseases.

This Special Issue aims to provide a comprehensive overview of current advances in the functional genomics of rare variants, with a focus on elucidating their biological impact and clinical relevance. We welcome contributions addressing experimental and computational approaches to variant characterization, including in vitro and in vivo functional assays, genome editing strategies, transcriptomic and epigenomic profiling, and integrative multi-omics analyses. We particularly encourage submissions that combine experimental and computational approaches to address the functional impact of rare variants. Despite these advances, a substantial proportion of rare variants identified through sequencing approaches remains of uncertain significance, highlighting the need for robust functional validation frameworks.

Particular emphasis will be placed on studies investigating rare variants in neurodevelopmental disorders, cancer predisposition, and other Mendelian and complex diseases, as well as on the development of novel frameworks for variant prioritization and pathogenicity assessment. Contributions exploring the interplay between rare variants, regulatory elements, and gene networks are also encouraged.

By bridging the gap between variant discovery and functional interpretation, this Special Issue aims to advance our understanding of disease mechanisms and to support the translation of genomic data into clinically actionable insights and precision medicine. 

Prof. Dr. Salvatore Saccone
Guest Editor

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Keywords

  • rare genetic variants
  • functional genomics
  • variant interpretation
  • next-generation sequencing
  • genome editing
  • neurodevelopmental disorders
  • Mendelian diseases
  • multi-omics integration
  • gene regulation
  • precision medicine

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Published Papers (1 paper)

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15 pages, 5470 KB  
Case Report
RFX3 Pathogenic Variants as a Rare Cause of Infantile Epileptic Spasms Syndrome
by Graziana Ceraolo, Giulia Spoto, Marina Trivisano, Concetta Federico, Mirella Vinci, Francesco Calì, Simone Treccarichi, Antonino Musumeci, Gabriella Di Rosa, Nicola Specchio and Antonio Gennaro Nicotera
Int. J. Mol. Sci. 2026, 27(16), 7238; https://doi.org/10.3390/ijms27167238 - 13 Aug 2026
Viewed by 370
Abstract
Regulatory Factor X3 (RFX3—OMIM#601337) encodes a transcription factor that is highly expressed in the human brain, particularly during neurodevelopment. It has been previously associated with neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual developmental disorder, and attention-deficit/hyperactivity disorder. However, the neurological and epileptic [...] Read more.
Regulatory Factor X3 (RFX3—OMIM#601337) encodes a transcription factor that is highly expressed in the human brain, particularly during neurodevelopment. It has been previously associated with neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual developmental disorder, and attention-deficit/hyperactivity disorder. However, the neurological and epileptic features remain poorly characterized, and no phenotype has yet been formally annotated in OMIM. Here, we report the second known case of Infantile Epileptic Spasms Syndrome (IESS) associated with RFX3 variants. The patient developed clusters of extensor spasms associated with eye deviation and achieved complete remission within two weeks following vigabatrin and ACTH therapy, remaining seizure-free thereafter. During follow-up, he presented with global developmental delay, ASD, and facial dysmorphisms. Genetic analysis by array comparative genomic hybridization identified a de novo heterozygous microdeletion of approximately 147 kb at 9p24.2, involving the initial exons of RFX3 (NM_134428). This case expands the clinical spectrum associated with RFX3 variants, supporting a potential role in IESS and early neurodevelopmental disruption. It highlights the relevance of including RFX3 in the genetic evaluation of patients with IESS and co-occurring neurodevelopmental disorders. Full article
(This article belongs to the Special Issue Functional Genomics of Rare Variants in Human Disease)
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