ClinVar Miner

Submissions for variant NM_001170629.2(CHD8):c.7258C>T (p.Arg2420Cys)

gnomAD frequency: 0.00001  dbSNP: rs371294659
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001270821 SCV001451585 uncertain significance Autism spectrum disorder 2020-06-19 criteria provided, single submitter clinical testing The CHD8 c.7258C>T (p.Arg2420Cys) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is found at a frequency of 0.000086 in the East Asian population of the Genome Aggregation Database in a region of good sequence coverage, but is based on one allele only, so the variant is presumed to be rare. Based on the limited evidence, the p.Arg2420Cys variant is classified as a variant of uncertain significance for autism spectrum disorder.
GeneDx RCV001655710 SCV001871013 uncertain significance not provided 2021-07-12 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533)
Labcorp Genetics (formerly Invitae), Labcorp RCV001655710 SCV002159026 uncertain significance not provided 2021-12-03 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 989319). This variant has not been reported in the literature in individuals affected with CHD8-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 2420 of the CHD8 protein (p.Arg2420Cys). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002375319 SCV002672488 uncertain significance Inborn genetic diseases 2018-01-22 criteria provided, single submitter clinical testing The p.R2420C variant (also known as c.7258C>T), located in coding exon 37 of the CHD8 gene, results from a C to T substitution at nucleotide position 7258. The arginine at codon 2420 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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