ClinVar Miner

Submissions for variant NM_001006658.2(CR2):c.3187C>T (p.Arg1063Cys) (rs145499318)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000650306 SCV000772147 uncertain significance Common variable immunodeficiency 7 2019-12-11 criteria provided, single submitter clinical testing This sequence change replaces arginine with cysteine at codon 1063 of the CR2 protein (p.Arg1063Cys). The arginine residue is weakly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs145499318, ExAC 0.1%). This variant has been observed in an individual with common variable immune deficiency (CVID) and decreased memory B cells with an exhausted B cell phenotype (CD21dim) (Invitae). ClinVar contains an entry for this variant (Variation ID: 540312). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000650306 SCV001190384 uncertain significance Common variable immunodeficiency 7 2019-06-20 criteria provided, single submitter clinical testing CR2 NM_001006658.2 exon 18 p.Arg1063Cys (c.3187C>T): This variant has not been reported in the literature but is present in 0.09% (28/30602) of South Asian alleles in the Genome Aggregation Database, including one homozygote (https://gnomad.broadinstitute.org/variant/1-207653397-C-T). This variant is present in ClinVar (Variation ID:540312). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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