ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.6184C>T (p.Arg2062Trp) (rs886063038)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000385958 SCV000474472 uncertain significance CHARGE association 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000296244 SCV000474473 uncertain significance Hypogonadotropic hypogonadism 5 with or without anosmia 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000485316 SCV000573498 likely pathogenic not provided 2017-02-23 criteria provided, single submitter clinical testing The R2062W variant in the CHD7 gene has been reported previously in an individual with CHARGE syndrome who also harbored a CHD7 nonsense variant; therefore the R2062W variant was presumed benign (Janssen et al., 2012). However, R2062W is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R2062W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret R2062W as a likely pathogenic variant.

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