De Novo Mutation in KMT2C Manifesting as Kleefstra Syndrome 2: Case Report and Literature Review

Round 1

Reviewer 1 Report

The case study describes a novel KMT2C variant in a patient with Kleefstra Syndrome 2. Case reports in rare diseases can support both genotype and phenotype characterisation of the disorders. In the submitted manuscript there are aspects that would benefit from clarification and additional supportive evidence to proceed to publication.

The KMT2C variant identified in this patient, c.9244C>T (p.Pro3082Ser) appears to be novel. However, other KMT2C p.3082 missense variants are known; in the gmomAD database (https://gnomad.broadinstitute.org/) p.Pro3082Leu has an allele count of 950, and p.Pro3082Arg has an allele count of 5. p.Pro3082Leu in particular has a sufficiently high anneal count that might suggest p.3082 missense variants may not be pathogenic. Can the authors provide further evaluation of their novel c.9244C>T (p.Pro3082Ser) variant, and supportive evidence that this KMT2C variant is indeed likely to be pathogenic and the cause of Kleefstra Syndrome 2 in this patient.

In the ‘Case presentation’ section, additional information and clarity would be useful for the following points:

• ‘high resolution array-CGH, which revealed a 2p16.3 microdeletion involving NRXN1’ – although the authors state that this has no clear pathogenic role, it would be useful to explain why they came to this conclusion.
• ‘Methylation and MLPA tests of chromosome 15q11-13 were normal’ – was this to rule out Angelman syndrome? If so, stating this would be helpful.
• On a related note, did molecular analysis of the genome reveal only a variant in KMT2C? It would be helpful to explain that other candidate genes were analysed (eg. MECP2, CDKL5, etc.) and no potential pathogenic variants were identified.
• It is stated that ‘parents did not show the variant’ – how was this verified?

Table 1 – the formatting of table 1 should be changed. In its current format, the text in the table is squashed and spread across multiple lines, making it extremely difficult for the reader to interpret.

Conclusion – in its present form, the conclusion lacks clarity, and should be improved to avoid repetitive words and make a clear statement.

Author Response

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Author Response File: Author Response.doc

Reviewer 2 Report

Line 42:  Was PRISMA guidelines for systematic review followed? If so, please mention it in this section. Add details about how many articles were found, how many were excluded, duplicated, and briefly mention the reason for exclusion.

Line 55: It would be better to include actual MRI images if possible.

Line 66: Elaborate on autistic traits.

Line 113: Please change the sentence structure to avoid the word "diagnosis" back-to-back twice.

Author Response

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Author Response File: Author Response.doc

Round 2

Reviewer 1 Report

Thank you to the authors for addressing the points raised in the initial review. These changes are welcome and improve the manuscript.
However, there are a couple of issues that would still be good to clarify, and include in the main body of the text, before the manuscript should be published. 
To address point 1, the authors state that "Whole exome sequencing of the patient and her parents was performed on genomic DNA obtained from peripheral blood leucocytes, identifying the de novo c.9244C>T; p.Pro3082Ser missense variant (see figure).  According to the Combined Annotation Dependent Depletion score (CADD score 22) and according to the American College of Medical Genetics score (PS2, PM2, PP3) (REF.PMID: 25741868) this variant can be considered as likely pathogenic."
It would extremely helpful if this text made it into the manuscript! In its current form, the manuscript does not explicitly state that exome sequencing was performed on the proband and the parents, so this statement helps clarify that, and supports the data. I think this statement is important to include. Also, the statement about the CADD score 22 is important to include in the main text of the manuscript and is supportive of the data. Adding a sentence to explain why the score of 22 suggests 'likely pathogenic' would also be beneficial.
This information is supportive of the conclusions and is extremely useful; and therefore, would significantly improve the clarity of the manuscript.
The conclusion has been expanded. However, the confusing sentences that were in the original conclusion are still present - I strongly recommend changing these for clarity. In line 2 of the conclusion: "Our study suggests that it must be taken in account in the differential diagnosis of a diagnosis of intellectual disability and/or autism spectrum disorder..." What does this mean? The newly added sentences in the conclusion are welcome, although the English (grammar and spelling) could be improved slightly for clarity.
Finally, the author list has been amended to include two new authors. What is the justification for adding two new authors at this late stage of the manuscript submission? Have these newly added authors contributed to the writing of the manuscript and/or analysis?
If these simple updates can be provided, I would recommend the manuscript could be published immediately.

Author Response

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Author Response File: Author Response.doc