Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The paper addresses an interesting and clinically relevant question concerning the phenotypic spectrum of the ultrarare MAPKBP1-associated nephronophthisis. The observation that scoliosis has been repeatedly reported among individuals with biallelic MAPKBP1 variants is noteworthy and deserves attention. However, several important methodological and analytical issues are present:
1. The primary disease cohort must be clearly defined: 21 or 19 patients? I couldn’t understand it from the Abstract. Two of the 21 individuals, P16 and P17, were subsequently reclassified as carrying a likely benign variant and a VUS, respectively, and were excluded from phenotype-frequency calculations. These individuals should therefore not be described as confirmed cases of MAPKBP1-related nephronophthisis. Check up the numbers in Abstract, Figure 2, Table 1, Results, Discussion, and Conclusions.
2. The manuscript should explicitly state how overlapping cohorts were identified and deduplicated. This is essential because even one or two duplicated patients could substantially alter a frequency estimated from only 19 individuals.
3. The search strategy requires revision. The search should include relevant synonyms, particularly JNKBP1, NPHP20, and potentially combinations with nephronophthisis/ciliopathy. Restricting the structured database search to “MAPKBP1” risks missing older literature using alternative nomenclature.
Additionally, the PROSPERO registration occurred on 23 June 2026 and the search extended through 30 June 2026. The authors should explicitly state that registration preceded screening/data extraction and describe any deviations from the registered protocol.
4. Methods state that JBI Critical Appraisal Tools for case reports and case series were applied. However, no study-level appraisal results are presented in the Results. Please, add a corresponding Table, provide item-level judgments; an overall summary of methodological limitations; number of reviewers; method used to resolve disagreement; ideally inter-reviewer agreement. Also, you have to use quality assessment in your Discussion.
5. The reported phenotype frequencies should not be interpreted as prevalence estimates. The authors correctly acknowledge that it was often impossible to determine whether a manifestation was truly absent or simply not investigated. Despite this, you calculate frequencies such as scoliosis: 8/19 = 42.1%; etc. for short stature and others. For rare-disease case reports, missing phenotypic information is usually strongly non-random: authors preferentially report unusual positive features, whereas normal orthopedic, cardiovascular, or craniofacial findings are often omitted.
6. The observation that scoliosis was reported in 8 of 19 genetically supported MAPKBP1 cases is potentially important. However, the formal comparison with a pooled prevalence of idiopathic scoliosis in the general population is not methodologically justified. The MAPKBP1 cohort is a literature-derived collection of selected cases rather than a population-based or prospectively ascertained cohort; musculoskeletal phenotyping was not standardized, and unreported scoliosis cannot be assumed to be absent. Moreover, the comparator represents idiopathic scoliosis in a different population, whereas MAPKBP1 patients include both children and adults and may have CKD-mineral and bone disorder and other causes of secondary skeletal abnormalities. Consequently, the calculated RR, OR, and exact binomial p value convey unjustified epidemiological precision and should be removed. The authors may retain the observed proportion with its exact confidence interval and state descriptively that scoliosis appears recurrent and warrants prospective systematic evaluation. Also, short-stature comparison has the same problem
8. Check up Table 2.The variant c.3578_3579del, p.Val1193Alafs*10 is classified as “Splicing.” Isn’t it a frameshift variant?
9. Clinical surveillance recommendations are currently stronger than the evidence warrants. Please, soften them. 
10. The term “NHP20” in the Abstract should be corrected to “NPHP20.”

Author Response

We thank the reviewer for taking the time to review this manuscript. Please find the detailed responses below and the corresponding corrections highlighted in track changes in the re-submitted files.

Comment 1: The primary disease cohort must be clearly defined: 21 or 19 patients? I couldn’t understand it from the Abstract. Two of the 21 individuals, P16 and P17, were subsequently reclassified as carrying a likely benign variant and a VUS, respectively, and were excluded from phenotype-frequency calculations. These individuals should therefore not be described as confirmed cases of MAPKBP1-related nephronophthisis. Check up the numbers in Abstract, Figure 2, Table 1, Results, Discussion, and Conclusions.

Response 1: Thank you for the suggestion; the numbers were actually confusing. We specified the final number (19) in all sections, leaving the two excluded cases as “uncertain/unconfirmed”. We also modified Figure 1 on order to better illustrate the selection process.

 

Comment 2: The manuscript should explicitly state how overlapping cohorts were identified and deduplicated. This is essential because even one or two duplicated patients could substantially alter a frequency estimated from only 19 individuals.

Response 2: The deduplication was performed manually (feasible, due to the moderate number of records), also comparing the variants from ClinVar. We added a paragraph in the Selection Process in Methods to briefly explain the procedure used to eliminate duplicates.

 

Comment 3: The search strategy requires revision. The search should include relevant synonyms, particularly JNKBP1, NPHP20, and potentially combinations with nephronophthisis/ciliopathy. Restricting the structured database search to “MAPKBP1” risks missing older literature using alternative nomenclature. 
Additionally, the PROSPERO registration occurred on 23 June 2026 and the search extended through 30 June 2026. The authors should explicitly state that registration preceded screening/data extraction and describe any deviations from the registered protocol.

Response 3: We thank the Reviewer for this important suggestion. To increase the sensitivity of the literature search and account for alternative gene and disease nomenclature, we expanded the search strategy to include “JNKBP1” and “NPHP20”. The search syntax was: “MAPKBP1” OR “JNKBP1” OR “NPHP20”. The expanded search was conducted in PubMed, Embase, and Google Scholar, and all potentially relevant retrieved records were screened according to the predefined eligibility criteria. The expanded search did not identify any additional eligible clinical reports or previously unidentified patients carrying biallelic MAPKBP1 variants. The relevant MAPKBP1-related studies retrieved using the additional terminology had already been identified and considered in the original review, while the remaining records did not meet the eligibility criteria. Therefore, the expanded search did not result in any changes to the composition of the clinical cohort. Section 2.2 (Search Strategy) has been revised accordingly to describe the expanded search strategy and its timing. There is also a statement explaining this and other deviations from the original PROSPERO protocol, that was written before the screening process.

 

Comment 4: Methods state that JBI Critical Appraisal Tools for case reports and case series were applied. However, no study-level appraisal results are presented in the Results. Please, add a corresponding Table, provide item-level judgments; an overall summary of methodological limitations; number of reviewers; method used to resolve disagreement; ideally inter-reviewer agreement. Also, you have to use quality assessment in your Discussion.

Response 4: As stated, JBI tools were used for quality assessment and risk of bias. The results were not originally submitted, but as suggested we agreed to make them available in the Supplemetary data for clarity and transparency. We expanded this section in the Methods and added two dedicated tables in the Supplementary material (Table S3 and S4). Results of these assessments and limitations were reported in the Results section and commented in the Discussion section.

 

Comment 5: The reported phenotype frequencies should not be interpreted as prevalence estimates. The authors correctly acknowledge that it was often impossible to determine whether a manifestation was truly absent or simply not investigated. Despite this, you calculate frequencies such as scoliosis: 8/19 = 42.1%; etc. for short stature and others. For rare-disease case reports, missing phenotypic information is usually strongly non-random: authors preferentially report unusual positive features, whereas normal orthopedic, cardiovascular, or craniofacial findings are often omitted.

Response 5: Thank you for this relevant comment. We corrected the statement, presenting the frequencies as related to "genetically eligible" patients (as suggested by other reviewers) and clarifying that all patients underwent at least an external clinical evaluation (as emerged from Quality Assessment, question Q5). This limitation is now discussed and the absence of specific exams is recognized as possible source of bias, as reported in Table S3 and S4.

 

Comment 6: The observation that scoliosis was reported in 8 of 19 genetically supported MAPKBP1 cases is potentially important. However, the formal comparison with a pooled prevalence of idiopathic scoliosis in the general population is not methodologically justified. The MAPKBP1 cohort is a literature-derived collection of selected cases rather than a population-based or prospectively ascertained cohort; musculoskeletal phenotyping was not standardized, and unreported scoliosis cannot be assumed to be absent. Moreover, the comparator represents idiopathic scoliosis in a different population, whereas MAPKBP1 patients include both children and adults and may have CKD-mineral and bone disorder and other causes of secondary skeletal abnormalities. Consequently, the calculated RR, OR, and exact binomial p value convey unjustified epidemiological precision and should be removed. The authors may retain the observed proportion with its exact confidence interval and state descriptively that scoliosis appears recurrent and warrants prospective systematic evaluation. Also, short-stature comparison has the same problem.

Response 6: Thank you for this observation, we agree that the comparison was not entirely justified. We decided to follow the suggestion and retain only the observed proportion and cinfidence interval, hinting that scoliosis and short stature appear to be recurrent in the cohort. For completeness, we mantained the reference for idiopathic scoliosis in the general population, but we specified the impossibility to compare the two cohorts.

 

Comment 7: Check up Table 2.The variant c.3578_3579del, p.Val1193Alafs*10 is classified as “Splicing.” Isn’t it a frameshift variant?

Response 7: The typo has been corrected.

 

Comment 8: Clinical surveillance recommendations are currently stronger than the evidence warrants. Please, soften them. 

Response 8: We thank the Reviewer for this comment. We agree that the available evidence is currently insufficient to support formal clinical surveillance recommendations. We have therefore revised the Conclusions to moderate the clinical implications of our findings. Rather than recommending systematic surveillance, we now emphasize clinical awareness of possible skeletal manifestations and the need for prospective studies with standardized phenotyping to determine whether specific surveillance strategies may be warranted 

Comment 9: The term “NHP20” in the Abstract should be corrected to “NPHP20.” 

Response 9: Thank you for noticing this typo. “NHP20” has been corrected to “NPHP20” in the Abstract.

The abstract itself was reorganized entirely following the PRISMA checklist for abstracts.

 

Reviewer 2 Report

Comments and Suggestions for Authors

This systematic review addresses an interesting and clinically relevant question regarding the possible expansion of the phenotypic spectrum of MAPKBP1-related nephronophthisis beyond renal manifestations. Given the rarity of NPHP20, the systematic aggregation of published clinical and molecular data is valuable. In particular, the attempt to integrate clinical observations with current knowledge regarding ciliary/JNK signaling provides an interesting framework for future studies.

The manuscript is generally well organized and potentially suitable for publication. However, several important methodological and interpretative issues should be addressed before the conclusions regarding extrarenal manifestations, particularly scoliosis, can be considered sufficiently robust.

Major comments

1. The definition of the study population requires clarification, particularly regarding P16 and P17

The manuscript states that 21 patients with biallelic MAPKBP1 variants were identified, and the Abstract refers to these individuals as patients with “MAPKBP1-related nephronophthisis.” However, the authors subsequently reclassified the variants in P16 and P17 as likely benign and variant of uncertain significance, respectively, and excluded these two patients when calculating phenotype frequencies.

This creates an important conceptual inconsistency. If the variants are currently considered likely benign or of uncertain significance, these individuals cannot be regarded with the same level of confidence as genetically confirmed MAPKBP1-related nephronophthisis cases.

I suggest defining the primary analytic cohort as the 19 patients carrying pathogenic/likely pathogenic variants and presenting the two patients with VUS/likely benign variants separately as excluded or uncertain cases. The Abstract, Results, Table 1, Figure 2, and Discussion should use consistent denominators and terminology throughout.

In particular, statements such as “21 patients with MAPKBP1-related nephronophthisis” should be reconsidered if two of these individuals do not meet the authors' own current molecular criteria for pathogenicity.

2. The comparison of scoliosis prevalence with the general population should be interpreted much more cautiously

The observation that scoliosis was reported in 8 of 19 patients is interesting and may indeed suggest a recurrent extrarenal phenotype. However, comparison with a pooled prevalence of idiopathic scoliosis in the general population, followed by calculation of an RR of 25.52, OR of 43.35, and a one-sided p-value of 3.53 × 10−10, may give an unjustified impression of statistical precision.

The 19 patients were assembled from case reports, families, sequencing cohorts, and database submissions rather than from a systematically phenotyped population-based cohort. Importantly:

• absence of scoliosis was not necessarily actively assessed in every patient;
• patients with unusual extrarenal manifestations may be more likely to be reported;
• several patients belong to the same families and therefore observations are not fully independent;
• the cohort includes both children and adults with markedly different opportunities to develop scoliosis;
• chronic kidney disease–mineral and bone disorder, secondary hyperparathyroidism, growth abnormalities, and other CKD-related factors may contribute to spinal deformity;
• the external comparator concerns idiopathic scoliosis, whereas scoliosis occurring in chronic kidney disease or a genetic syndrome is not necessarily etiologically comparable.

The authors acknowledge several of these limitations, which is appreciated. Nevertheless, I would strongly suggest treating the comparison with the general population as descriptive/exploratory rather than as formal evidence of association. Consider removing or substantially de-emphasizing the RR, OR, and particularly the one-sided hypothesis test. The recurrence of scoliosis across unrelated cases is itself an important finding and can be presented without implying an accurately quantified excess risk.

3. Please provide the results of the risk-of-bias/quality assessment

The Methods state that JBI Critical Appraisal Tools for Case Reports and Case Series were used. However, the results of this assessment are not clearly presented.

Please provide the appraisal results for each included clinical report, preferably in a supplementary table. It should also be explained how study quality influenced interpretation of individual phenotypic findings.

This is particularly important because the central conclusion of the review is based predominantly on case reports and small case series, for which selective reporting and incomplete phenotyping are major concerns.

4. The literature search strategy should be reported in sufficient detail to permit reproducibility

The authors searched PubMed, Embase, ClinVar, Google Scholar, and reference lists and used “MAPKBP1” as the principal search term. This broad approach is understandable for an ultrarare disorder. However, the exact search strategy should be reproducible.

Please provide, preferably in Supplementary Materials:

• the complete PubMed search syntax;
• the complete Embase search syntax;
• the exact dates on which each database was searched;
• any language or publication-type restrictions;
• the ClinVar search strategy and date of access;
• the procedure used for duplicate removal;
• the method used for screening and resolving disagreements between reviewers;
• sufficient detail regarding the Google Scholar search, including how the “first 100 results” were ordered and screened.

The manuscript states that PRISMA 2020 was followed and that the protocol was prospectively registered in PROSPERO, which are strengths. The final report should therefore provide a fully reproducible search strategy consistent with PRISMA reporting.

5. Please reconcile the PRISMA flow diagram and the description of study selection

The study selection should be checked carefully for numerical consistency between the text and Figure 1.

The Results state that 63 records were identified through electronic database searching, 26 duplicates were removed, 37 records were screened, 24 full texts were assessed, 14 experimental studies were excluded, and 10 reports remained, with two additional reports identified through other methods.

However, the right-hand pathway of the PRISMA diagram appears to indicate additional numbers of records/reports that are not immediately intuitive from the accompanying text. Please ensure that all numbers in the PRISMA diagram reconcile exactly with the narrative description and clearly distinguish database records, ClinVar entries, citation searching, Google Scholar records, and final included reports.

6. The denominator for each phenotype should reflect whether the feature was actually assessed

The authors correctly recognize that an unreported feature cannot necessarily be interpreted as an absent feature. This issue is central to the manuscript.

Nevertheless, most frequencies are calculated using 19 patients as the denominator. For example, scoliosis is reported as 8/19 (42.1%) and short stature/growth delay as 5/19 (26.3%). If spinal examination, height measurement, cardiovascular evaluation, or other relevant assessments were not explicitly performed in every patient, these denominators may underestimate or distort the true frequency.

Where possible, I suggest distinguishing among:

1. feature explicitly present;
2. feature explicitly assessed and absent;
3. feature not reported/not assessed.

If the original reports do not allow this distinction reliably, the authors should avoid describing 8/19 as an estimated prevalence and instead use wording such as “scoliosis was reported in 8 of 19 genetically eligible patients.” This distinction would considerably strengthen the interpretation.

7. The mechanistic link between MAPKBP1 deficiency and the skeletal phenotype should remain clearly hypothesis-generating

The discussion linking MAPKBP1, ciliary localization, JNK signaling, TGF-β/TAK1 signaling, osteoblast differentiation, and scoliosis is biologically interesting. However, the available evidence does not directly demonstrate that MAPKBP1 deficiency causes scoliosis through this pathway.

The manuscript itself appropriately notes that functional studies in MAPKBP1-deficient bone-lineage cells are required. I recommend ensuring that the entire mechanistic discussion consistently distinguishes established observations from biological hypotheses. A schematic model identifying confirmed versus proposed relationships could also be helpful if the authors wish to retain the detailed mechanistic discussion.

8. Recommendations for clinical surveillance should be moderated

The Conclusion states that the available clinical and molecular evidence is sufficient to improve follow-up strategies and recommends systematic assessment and management of scoliosis, growth delay, and other skeletal manifestations.

Given that only 19 molecularly convincing cases appear to be available and phenotyping was retrospective and non-standardized, the evidence may not yet support formal surveillance recommendations.

It would be more appropriate to state that clinicians should be aware of possible skeletal manifestations and that prospective standardized orthopedic assessment should be considered in future cohorts. The distinction between reasonable clinical awareness and an evidence-based surveillance protocol is important.

Minor comments

1. Please check section numbering. The manuscript proceeds from Section 1.3 to Section 1.5, and from Section 3 to Section 5. Sections 1.4 and 4 appear to be missing.
2. The terminology “extrarenal” and “extra-renal” should be standardized throughout the manuscript.
3. Please standardize the terminology “variant of uncertain significance (VUS)” rather than “VoUS,” unless the latter is specifically required by the journal.
4. Table 1 is informative, but it would be helpful to clearly identify which patients are included in the primary phenotype analysis and visually separate patients carrying P/LP variants from those carrying VUS/likely benign variants.
5. Figure 2 is visually useful, but the label “Total patients n = 21” may be misleading because the principal frequency calculations exclude P16 and P17. The figure should either represent the 19 molecularly eligible patients or clearly distinguish the two uncertain cases.
6. For the newly submitted ClinVar patient (P12), please clearly distinguish data derived from the public database entry from additional unpublished clinical information obtained directly by the authors. Because extensive clinical information is provided for this patient, the source of each type of information should be transparent.
7. The statement that no significant difference in extrarenal manifestations was observed between patients investigated by exome sequencing and those investigated by other methods (p = 0.62) should be interpreted cautiously. With such a small sample, absence of statistical significance cannot establish equivalence between testing strategies.
8. The suggestion that missense variants may be associated with milder disease is based on extremely few individuals. This should remain explicitly hypothesis-generating.
9. Please carefully proofread the manuscript. There are several typographical or formatting issues, for example “butwere,” “reportswere,” “Herequired,” and errors in the Author Contributions section.
10. The Supplementary Materials section still contains template placeholders (“Figure S1: title; Table S1: title; Video S1: title”). These should be corrected or removed before publication.

Overall assessment

This review addresses an ultrarare disorder for which systematic aggregation of individual cases is genuinely useful. The identification of recurrent skeletal abnormalities, particularly scoliosis, is noteworthy and deserves publication and further investigation.

The main issue is not the observation itself but the strength with which the available case-based evidence is currently interpreted. The manuscript would be considerably strengthened by defining the genetically confirmed cohort more rigorously, reporting the risk-of-bias assessment, improving reproducibility of the systematic-review methodology, reconsidering formal statistical comparisons with the general population, and moderating causal and clinical-surveillance conclusions.

With these revisions, the manuscript could provide a useful reference for clinicians and researchers working on MAPKBP1-related nephronophthisis and rare renal ciliopathies.

 

Author Response

We thank the reviewer for taking the time to analyze our paper and for the useful suggestions. Both the "track changes" and the "clean" version of the revised manuscript has been uploaded, here we report the responses to the comments.

 

Comment 1: The definition of the study population requires clarification, particularly regarding P16 and P17.

Response 1: Thank you for the suggestion; the numbers were actually confusing. We specified the final number (19) in all sections, leaving the two excluded cases as “uncertain/unconfirmed”. All sections were corrected, including the figures.

 

Comment 2: The comparison of scoliosis prevalence with the general population should be interpreted much more cautiously.

Response 2: We thank the Reviewer for this comment. We agree that the available evidence is currently insufficient to support formal clinical surveillance recommendations. We have therefore revised the Conclusions to moderate the clinical implications of our findings. Rather than recommending systematic surveillance, we now emphasize clinical awareness of possible skeletal manifestations and the need for prospective studies with standardized phenotyping to determine whether specific surveillance strategies may be warranted. We expanded the limitations and reported the frequencies without exact statistical calculations.

 

Comment 3: Please provide the results of the risk-of-bias/quality assessment

Response 3: As stated, JBI tools were used for quality assessment and risk of bias. The results were not originally submitted, but, as suggested, we agreed to make them available in the Supplemetary data for clarity and transparency. We expanded this section in the Methods and added two dedicated tables in the Supplementary material (Table S3 and S4). Results of these assessments and limitations were reported in the Results section and commented in the Discussion section.

 

Comment 4: The literature search strategy should be reported in sufficient detail to permit reproducibility

Response 4: The original search syntax was simply “MAPKBP1”, with no date restrictions or other filters. More recently, following specific comments (also from other reviewers), we have expanded the search and modified the Methods section accordingly, including the exact search syntax and more info for reproducibility (no new studies were included).

 

Comment 5: Please reconcile the PRISMA flow diagram and the description of study selection.

Response 5: The numbers reported in the narrative description have been reconciled with the one reported in the PRISMA flowchart. The Figure 1 (flowchart) has been updated, also considering the new search syntax. The methodological section has been implemented and the checklists from PRISMA have been added in the Supplementary material for clarity. Since the 2 articles cited by other papers were actually among the results of Google Scholar, we simplified those numbers; according to PRISMA indications, since Google Scholar was used for literature search, we moved it in the main source section (left side of the flow chart), allowing the insrtion of details about deduplication. Since ClinVar is not a literature database and the entries are not paper/abstracts but single variants, we moved it in the additional source (right side). All the numbers have been harmonized and the selection process is clearly explained in the Methods.

 

Comment 6: The denominator for each phenotype should reflect whether the feature was actually assessed.

Response 6: Thank you for this relevant comment. We corrected the statements, considering only patients who were actually investigated for the specific issue. This limitation is now discussed and the absence of specific exams is one of the constituents of the quality score and risk of bias, as reported in Table S3 and S4.

 

Comment 7: The mechanistic link between MAPKBP1 deficiency and the skeletal phenotype should remain clearly hypothesis-generating.

Response 7: We thank the Reviewer for this important comment. We have therefore substantially revised the Discussion to more clearly distinguish established disease-specific observations from the proposed biological hypothesis. Specifically, we now state that previous functional studies directly demonstrate altered ciliary localization of MAPKBP1, shortened primary cilia, and altered phosphorylated-JNK trafficking in MAPKBP1-deficient cellular models, whereas the studies addressing JNK and TAK1/p38 signaling in osteoblast differentiation provide only broader biological plausibility and do not directly involve MAPKBP1. The Conclusions have been revised accordingly. We also considered the Reviewer’s suggestion of adding a mechanistic schematic. However, because no direct experimental link between MAPKBP1 deficiency and skeletal disease has yet been demonstrated, we felt that a pathway diagram could inadvertently suggest a degree of mechanistic certainty that is not supported by the available evidence. We therefore chose instead to make the distinction between established and proposed relationships explicit in the text.

 

Comment 8: Recommendations for clinical surveillance should be moderated.

Response 8: We agree with the Reviewer that the limited number of molecularly confirmed cases and the retrospective, non-standardized nature of the available phenotypic data do not currently support formal evidence-based surveillance recommendations. Accordingly, we have revised the Conclusions to distinguish clinical awareness from formal surveillance recommendations. We now suggest that clinicians should be aware of possible skeletal manifestations in MAPKBP1-related nephronophthisis, while emphasizing that prospective studies with standardized orthopedic phenotyping are required to establish their frequency and clinical relevance and to determine whether specific surveillance strategies are warranted.

 

Minor comments 

1) Please check section numbering. The manuscript proceeds from Section 1.3 to Section 1.5, and from Section 3 to Section 5. Sections 1.4 and 4 appear to be missing. 

-Thank you for pointing this out. The section numbering has been corrected throughout the manuscript. 

 

2) The terminology “extrarenal” and “extra-renal” should be standardized throughout the manuscript. 

-The terminology has been standardized to “extrarenal” throughout the manuscript 

 

3) Please standardize the terminology “variant of uncertain significance (VUS)” rather than “VoUS,” unless the latter is specifically required by the journal. 

-The terminology has been standardized to “variant of uncertain significance (VUS)” throughout the manuscript. 

 

4) Table 1 is informative, but it would be helpful to clearly identify which patients are included in the primary phenotype analysis and visually separate patients carrying P/LP variants from those carrying VUS/likely benign variants. 

- We thank the Reviewer for this suggestion. Table 1 has been revised to clearly distinguish the 19 molecularly eligible patients included in the primary phenotype analysis from P16 and P17. The latter are now explicitly identified as patients carrying variants reclassified as ACMG Class 3 or Class 2 and excluded from the primary phenotype analysis. 

5) Figure 2 is visually useful, but the label “Total patients n = 21” may be misleading because the principal frequency calculations exclude P16 and P17. The figure should either represent the 19 molecularly eligible patients or clearly distinguish the two uncertain cases. 

- We thank the Reviewer for this observation. Figure 2 has been revised to represent only the 19 molecularly eligible patients included in the primary phenotype analysis. 

 

6) For the newly submitted ClinVar patient (P12), please clearly distinguish data derived from the public database entry from additional unpublished clinical information obtained directly by the authors. Because extensive clinical information is provided for this patient, the source of each type of information should be transparent. 

- We agree and we specified that additional information was obtained by contacting the clinicians who took care of the patient in our Hospital (they were already included in the authors) and by retrieving official medical reports. 

 

7) The statement that no significant difference in extrarenal manifestations was observed between patients investigated by exome sequencing and those investigated by other methods (p = 0.62) should be interpreted cautiously. With such a small sample, absence of statistical significance cannot establish equivalence between testing strategies. 

- We thank the Reviewer for this important observation. We agree that the absence of a statistically significant difference cannot be interpreted as evidence of equivalence between patients investigated by exome sequencing and those investigated using other methods, particularly given the small sample size. We have therefore revised the corresponding statement and remove specific statistical comparisons. 

 

8) The suggestion that missense variants may be associated with milder disease is based on extremely few individuals. This should remain explicitly hypothesis-generating. 

- We modified the statement as purely hypothesis-generating. 

 

9) Please carefully proofread the manuscript. There are several typographical or formatting issues, for example “butwere,” “reportswere,” “Herequired,” and errors in the Author Contributions section. 

- The manuscript has been carefully proofread, and the indicated typographical and formatting errors have been corrected 

 

10) The Supplementary Materials section still contains template placeholders (“Figure S1: title; Table S1: title; Video S1: title”). These should be corrected or removed before publication. 

- Yes, that was going to be corrected, once clearly defined the need of Supplementary material. Now it has been modified accordingly.

 

Reviewer 3 Report

Comments and Suggestions for Authors

This systematic review provides a useful summary of the currently available clinical and molecular evidence regarding MAPKBP1-related nephronophthisis, with particular emphasis on possible extrarenal manifestations. The manuscript is generally well organized and clinically relevant. A few minor points should be addressed to further improve the manuscript.

1. The authors mention that they assessed the quality and risk of bias of the included studies using the JBI Critical Appraisal Tools. It would be useful to see the actual results of this assessment, ideally as a supplementary table, so readers can judge the quality of the evidence for themselves.
2. The comparison of scoliosis prevalence against the general population needs to be interpreted with more caution. With such a small number of patients and the fact that the cases were collected retrospectively from published reports and databases, ascertainment and reporting bias are likely to have influenced the observed frequency. I would suggest the authors make it clearer that the calculated RR, OR and P value are exploratory rather than definitive evidence of an association.
3. In the Discussion the authors suggest a possible link between MAPKBP1 deficiency, altered ciliary/JNK signalling and skeletal abnormalities such as scoliosis. Some of the cited papers mainly discuss the broader roles of JNK/TAK1 signalling in osteoblast differentiation, rather than any direct involvement of MAPKBP1 in skeletal disease. It would be helpful if the authors checked that their statements are properly supported by the references and more clearly separated established findings from their proposed mechanistic hypothesis.

Author Response

We thank the reviewer for the useful comments, to which we replied below. A track-changes version and a clean version of the manuscript is being submitted.

Comment 1: The authors mention that they assessed the quality and risk of bias of the included studies using the JBI Critical Appraisal Tools. It would be useful to see the actual results of this assessment, ideally as a supplementary table, so readers can judge the quality of the evidence for themselves.

Response 1: Thank you for the suggestion, we added two specific tables in the Supplementary material and we expanded the Results and Discussion to comment the issues emerged from quality and bias assessment.

Comment 2: The comparison of scoliosis prevalence against the general population needs to be interpreted with more caution. With such a small number of patients and the fact that the cases were collected retrospectively from published reports and databases, ascertainment and reporting bias are likely to have influenced the observed frequency. I would suggest the authors make it clearer that the calculated RR, OR and P value are exploratory rather than definitive evidence of an association.

Response 2: We thank the reviewer for this comment. Only the observed frequencies were retained, hinting that scoliosis and short stature appear to be recurrent in the cohort.  In general, the data have been now reported with caution considering the limitations (see Results and Discussion).

 

Comment 3: In the Discussion the authors suggest a possible link between MAPKBP1 deficiency, altered ciliary/JNK signalling and skeletal abnormalities such as scoliosis. Some of the cited papers mainly discuss the broader roles of JNK/TAK1 signalling in osteoblast differentiation, rather than any direct involvement of MAPKBP1 in skeletal disease. It would be helpful if the authors checked that their statements are properly supported by the references and more clearly separated established findings from their proposed mechanistic hypothesis.

Response 3: We thank the Reviewer for this helpful comment. We have revised the Discussion and Conclusion sections to more clearly distinguish the available experimental evidence from the proposed interpretation of the skeletal phenotype. In particular, we have moderated the mechanistic statements and clarified that the possible link between altered MAPKBP1-related ciliary/JNK signaling and scoliosis remains hypothetical. The revised text now emphasizes that the cited studies support biological plausibility, but that direct evidence connecting MAPKBP1 deficiency to skeletal abnormalities is currently lacking.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The revision is clearly improved, but several responses claim that an issue has been resolved when the revised text still contains the same problem, or a closely related one. 

1. The Abstract is currently inconsistent with the actual PRISMA flow diagram and Results. The Abstract states 122 records identified; …; 19 patients. Section 3.1 states 154 records identified; …; 9 studies included. 
2. The Abstract says: “All included reports were judged to be of high or moderate methodological quality and at low risk of bias.” Yet Results state: “Only one paper was considered at high risk of bias, while 7 articles or database entries had a moderate risk.”
3. The problem 19 vs 21 still exists: “Altogether, the 21 patients carried a total of 19 variants...”
4. The Discussion still states that scoliosis is “becoming evident” to be more frequent, then compares 42.1% in MAPKBP1 cases with 1.65% idiopathic scoliosis prevalence and calls the MAPKBP1 value “definitively higher” while simultaneously admitting that “the two cohorts are not directly comparable.” That is logically inconsistent. 
5. In the response of comment 8: the authors no longer recommend systematic surveillance and instead emphasize awareness and future prospective studies. But the Abstract still says “patients with NPHP20 may benefit from multidisciplinary surveillance extending beyond renal manifestations.” And the Conclusion is even stronger.
6. I also recommend revisiting the proposed MAPKBP1 carrier-frequency calculation, particularly whether non-pathogenic/VUS variants were included and whether summed allele frequency has been appropriately converted to carrier frequency.

Author Response

We're sorry, but most of the highlighted issues are due to the wrong "track changes" file included in the uploaded .zip file. It was not possible to change the .doc file after submission... we emailed the journal with the correct "track changes" version, but it was probably too late. However, the uploaded PDF file was correct and already included most of the changes suggested here.

We took the opportunity to further improve the manuscript following the latest suggestions from the reviewer, thus we thank them for the patience and time spent for the review.

1) The numbers were already corrected in the clean and PDF version and are now consistent with the Results in all the versions of the file.

2) Thanks, it was actually an over-simplification for the sake of brevity, but it could actually affect the interpretation in a small cohort. We modified the abstract.

3) The numbers were already corrected in the clean and PDF version and are now consistent with the Table and following sections.

4) Thanks for the observation. We moderated the Discussion section as suggested and we eliminated the sentence concerning general population.

5) We have further softened the Conclusions and the Abstract as suggested.

6) We agree, the inclusion of VUS (even if reported in published patients) in Table 2 may lead to confusion and is not coherent with the main text. We updated the table and the numbers. Also, we revised the carrier frequency calculation, clearly distinguishing allele frequency and carrier frequency.

 

 

Reviewer 2 Report

Comments and Suggestions for Authors

I have carefully reviewed the revised manuscript. The authors have satisfactorily addressed the previous comments, and the manuscript is now clear, well organized, and methodologically sound. The conclusions are appropriately supported by the presented evidence. I have no further comments or suggestions and recommend acceptance in its present form.

Author Response

We are grateful to the reviewer.