ClinVar Miner

Submissions for variant NM_001271.4(CHD2):c.2095C>T (p.Arg699Trp)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000493748 SCV000582278 pathogenic not provided 2022-06-14 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31785789, 33004838)
Ambry Genetics RCV000623592 SCV000741687 uncertain significance Inborn genetic diseases 2016-11-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV000623592 SCV000847520 uncertain significance Inborn genetic diseases 2016-08-11 criteria provided, single submitter clinical testing The p.R699W variant (also known as c.2095C>T), located in coding exon 16 of the CHD2 gene, results from a C to T substitution at nucleotide position 2095. The arginine at codon 699 is replaced by tryptophan, an amino acid with dissimilar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6495 samples (12990 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Génétique des Maladies du Développement, Hospices Civils de Lyon RCV000505237 SCV000890059 likely pathogenic Developmental and epileptic encephalopathy 94 2017-07-12 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Strasbourg University Hospital RCV001260660 SCV001437752 pathogenic Intellectual disability 2020-09-10 criteria provided, single submitter clinical testing
Invitae RCV000505237 SCV002167677 pathogenic Developmental and epileptic encephalopathy 94 2023-08-16 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 699 of the CHD2 protein (p.Arg699Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of CHD2-related conditions (PMID: 31785789, 33004838; Invitae). In at least one individual the variant was observed to be de novo. This variant is also known as c.2134C>T (p.Arg712Trp) and 15:93510649C>T. ClinVar contains an entry for this variant (Variation ID: 429658). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CHD2 protein function. For these reasons, this variant has been classified as Pathogenic.
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals RCV000505237 SCV000599251 likely pathogenic Developmental and epileptic encephalopathy 94 2016-09-30 no assertion criteria provided clinical testing

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