ClinVar Miner

Submissions for variant NM_000448.3(RAG1):c.1981_1983del (p.Met661del)

gnomAD frequency: 0.00002  dbSNP: rs774103837
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001234668 SCV001407325 pathogenic Combined immunodeficiency with skin granulomas; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2024-10-22 criteria provided, single submitter clinical testing This variant, c.1981_1983del, results in the deletion of 1 amino acid(s) of the RAG1 protein (p.Met661del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs774103837, gnomAD 0.01%). This variant has been observed in individual(s) with clinical features of severe combined immunodeficiency (internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 961035). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002069307 SCV002495915 uncertain significance Combined immunodeficiency due to partial RAG1 deficiency; Combined immunodeficiency with skin granulomas; Histiocytic medullary reticulosis; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2022-02-08 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in 0.01% (4/34578) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/11-36596834-TATG-T?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:961035). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant represents an in frame deletion of 1 amino acid at position 661 and is not predicted to alter the reading frame. However, the effect of this variant on the protein is unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Fulgent Genetics, Fulgent Genetics RCV002069307 SCV005683473 likely pathogenic Combined immunodeficiency due to partial RAG1 deficiency; Combined immunodeficiency with skin granulomas; Histiocytic medullary reticulosis; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2024-05-29 criteria provided, single submitter clinical testing

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