ClinVar Miner

Submissions for variant NM_006306.4(SMC1A):c.3497A>G (p.Asn1166Ser)

dbSNP: rs1556885810
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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 RCV000624551 SCV000741225 uncertain significance Inborn genetic diseases 2015-12-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002531886 SCV003026057 likely pathogenic Congenital muscular hypertrophy-cerebral syndrome 2023-02-01 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1166 of the SMC1A protein (p.Asn1166Ser). This variant has not been reported in the literature in individuals affected with SMC1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 520894). 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 SMC1A protein function. This variant disrupts the p.Asn1166 amino acid residue in SMC1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24124034, 33619735). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV002531886 SCV004099219 likely pathogenic Congenital muscular hypertrophy-cerebral syndrome 2023-07-18 criteria provided, single submitter clinical testing PS2, PM2, PM5_Supporting, PP2, PP3

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