ClinVar Miner

Submissions for variant NM_001006658.3(CR2):c.3047C>T (p.Ser1016Leu)

gnomAD frequency: 0.00034  dbSNP: rs138062179
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000700990 SCV000829770 uncertain significance Immunodeficiency, common variable, 7 2022-10-25 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1016 of the CR2 protein (p.Ser1016Leu). This variant is present in population databases (rs138062179, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with CR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 578084). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.
Blueprint Genetics RCV000788315 SCV000927377 uncertain significance not provided 2017-08-14 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000788315 SCV002544358 uncertain significance not provided 2023-03-01 criteria provided, single submitter clinical testing CR2: PM2, BP4
Fulgent Genetics, Fulgent Genetics RCV002477612 SCV002793159 uncertain significance Systemic lupus erythematosus, susceptibility to, 9; Immunodeficiency, common variable, 2; Immunodeficiency, common variable, 7 2022-04-13 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004547868 SCV004116676 uncertain significance CR2-related disorder 2023-05-31 criteria provided, single submitter clinical testing The CR2 c.3047C>T variant is predicted to result in the amino acid substitution p.Ser1016Leu. This variant was reported in an individual with severe hypertension and renal microangiopathy (Patient 37, Larsen et al. 2017. PubMed ID: 29148534). This variant is reported in 0.052% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-207651374-C-T), which may be too common to be causative of disease. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Genome-Nilou Lab RCV000700990 SCV004180454 uncertain significance Immunodeficiency, common variable, 7 2023-04-11 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000788315 SCV005187187 uncertain significance not provided criteria provided, single submitter not provided

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