ClinVar Miner

Submissions for variant NM_000536.4(RAG2):c.14T>A (p.Met5Lys) (rs143415103)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000330271 SCV000371808 uncertain significance Histiocytic medullary reticulosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000387091 SCV000371809 uncertain significance Severe Combined Immune Deficiency 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000689525 SCV000817179 uncertain significance Combined cellular and humoral immune defects with granulomas; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2018-01-18 criteria provided, single submitter clinical testing This sequence change replaces methionine with lysine at codon 5 of the RAG2 protein (p.Met5Lys). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and lysine. This variant is present in population databases (rs143415103, ExAC 0.01%). This variant has not been reported in the literature in individuals with RAG2-related disease. ClinVar contains an entry for this variant (Variation ID: 304560). 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: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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