ClinVar Miner

Submissions for variant NM_001271.4(CHD2):c.3526C>A (p.Leu1176Met)

dbSNP: rs1555444216
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519265 SCV000621526 uncertain significance not provided 2017-10-12 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CHD2 gene. The L1176M variant hasnot been published as a pathogenic variant, nor has it been reported as a benign variant to ourknowledge. The L1176M variant is not observed in large population cohorts (Lek et al., 2016). TheL1176M variant is a conservative amino acid substitution, which is not likely to impact secondaryprotein structure as these residues share similar properties. However, this substitution occurs at aposition that is conserved across species, and in silico analysis predicts this variant is probablydamaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV003741197 SCV004463882 uncertain significance Developmental and epileptic encephalopathy 94 2023-05-12 criteria provided, single submitter clinical testing 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. 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 not expected to disrupt CHD2 protein function. ClinVar contains an entry for this variant (Variation ID: 452699). This variant has not been reported in the literature in individuals affected with CHD2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 1176 of the CHD2 protein (p.Leu1176Met).

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