R559S (p.Arg559Ser) variant of RAG1 (P15918)
R559S (p.Arg559Ser) in RAG1 (P15918) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as pathogenic in the context of Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-n. The available variant effect predictions contribute to a CATVariant prioritization score of 0.56 / 1. The record also includes population frequency data, published literature, and structural context.
R559S (p.Arg559Ser) variant details
- p.Arg559Ser
- rs199474681
- TOPMed rs199474681
- gnomAD rs199474681
- ClinGen CA219812
- Pathogenic
- Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-n
- Missense
- Variant Prioritization Score for Impact Estimate 0.556
- REVEL 0.79
- CADD 22.30
- PolyPhen-2 0.99
- SIFT 0.00
- ClinVar: Pathogenic (Combined immunodeficiency with skin granulomas; Severe combined)
- EBI: Pathogenic (in T(-)B(-)NK(+) SCID and OS)
- UniProt: Pathogenic (in T(-)B(-)NK(+) SCID and OS)
- Most common in the REMAINING population (allele frequency 3.3e-05)
- Structural context available
- Cited in: V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical… (PMID 11133745)
- Cited in: Identification of anti-herpes simplex virus antibody-producing B cells in a patient with an atypical RAG1… (PMID 11520796)