ClinVar Miner

Submissions for variant NM_003079.5(SMARCE1):c.767A>G (p.Lys256Arg)

gnomAD frequency: 0.00010  dbSNP: rs542193901
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000472542 SCV000546051 uncertain significance Familial meningioma 2024-01-13 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 256 of the SMARCE1 protein (p.Lys256Arg). This variant is present in population databases (rs542193901, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with SMARCE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 407070). 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 SMARCE1 protein function with a positive predictive value of 80%. 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.
Fulgent Genetics, Fulgent Genetics RCV000765350 SCV000896615 uncertain significance Familial meningioma; Coffin-Siris syndrome 5 2018-10-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV001026703 SCV001189134 likely benign Hereditary cancer-predisposing syndrome 2023-06-28 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Preventiongenetics, part of Exact Sciences RCV003409620 SCV004116396 uncertain significance SMARCE1-related condition 2023-04-19 criteria provided, single submitter clinical testing The SMARCE1 c.767A>G variant is predicted to result in the amino acid substitution p.Lys256Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0054% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-38787893-T-C). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Baylor Genetics RCV000472542 SCV004205033 uncertain significance Familial meningioma 2023-09-18 criteria provided, single submitter clinical testing

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