ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.5050G>A (p.Gly1684Ser)

dbSNP: rs1554602465
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000623724 SCV000741041 pathogenic Inborn genetic diseases 2015-09-25 criteria provided, single submitter clinical testing
Invitae RCV001382047 SCV001580653 pathogenic CHARGE association 2023-10-31 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1684 of the CHD7 protein (p.Gly1684Ser). This variant also falls at the last nucleotide of exon 22, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of CHARGE syndrome (PMID: 22461308, 22462537, 25077900, 27562378). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 520773). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001570011 SCV001794204 pathogenic not provided 2021-12-11 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 18089695, 22539353, 28566479, 28475860, 27562378, 25077900, 32326958, 22462537)

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