ClinVar Miner

Submissions for variant NM_000448.3(RAG1):c.2488A>T (p.Lys830Ter)

gnomAD frequency: 0.00002  dbSNP: rs755551812
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778323 SCV000914509 likely pathogenic RAG1-related disorder 2018-12-11 criteria provided, single submitter clinical testing The RAG1 c.2488A>T (p.Lys830Ter) variant is a stop-gained variant predicted to result in premature termination of the protein. The p.Lys830Ter variant has been reported in at least three studies and is found in a total of five individuals with RAG1-related disorders, including one homozygote, three compound heterozygotes and one heterozygote, all of whom carried a p.Arg829Ser variant in cis with the p.Lys830Ter variant (Santagata et al. 2000; Sobacchi et al. 2006; Haq et al. 2007). Additionally, Meshaal et al. (2015) described a c.2487_2488delGAinsTT variant, also resulting in a truncation of the protein at residue 830, in a homozygous state in an individual with severe combined immunodeficiency. Control data are unavailable for the p.Lys830Ter variant which is reported at a frequency of 0.00043 in the Latino population of the Exome Aggregation Consortium. Based on the evidence and potential impact of stop-gained variants, the p.Lys830Ter variant is classified as likely pathogenic for RAG1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Revvity Omics, Revvity RCV001784382 SCV002019638 pathogenic not provided 2020-12-18 criteria provided, single submitter clinical testing

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