Submissions for variant NM_000448.3(RAG1):c.2291G>A (p.Arg764His)

gnomAD frequency: 0.00001  dbSNP: rs768809293

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen	RCV003991482	SCV004809115	uncertain significance	Recombinase activating gene 1 deficiency	2024-02-26	reviewed by expert panel	curation	NM_000448.3(RAG1):c.2291G>A is a missense variant predicted to cause substitution of Arginine by Histidine at amino acid 764 (p.Arg764His). This missense variant is located in the core domain (amino acids 387-1011) (PM1_supporting). The filtering allele frequency (the upper threshold of the 95% CI of 22/1180042) of the c.2291G>A variant in RAG1 is 0.00001213 for European Non-Finnish chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.000102) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). Two missense variants c. 2291G>C, p.R764P (PMID: 24290284); c.2290C>T , p.Arg764Cys (PMID: 25104208) (not classified by SCID VCEP yet) in the same codon have been reported. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for autosomal recessive severe combined immunodeficiency due to RAG1 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PM1_supporting, PM2_Supporting (VCEP specifications version 1).
Labcorp Genetics (formerly Invitae), Labcorp	RCV001871951	SCV002178446	uncertain significance	Combined immunodeficiency with skin granulomas; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	2022-07-18	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 764 of the RAG1 protein (p.Arg764His). This variant is present in population databases (rs768809293, gnomAD 0.002%). This missense change has been observed in individual(s) with selective immunoglobulin A deficiency (PMID: 25739914). ClinVar contains an entry for this variant (Variation ID: 1050623). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RAG1 protein function. Experimental studies have shown that this missense change affects RAG1 function (PMID: 25739914). This variant disrupts the p.Arg764 amino acid residue in RAG1. Other variant(s) that disrupt this residue have been observed in individuals with RAG1-related conditions (PMID: 24290284, 25104208, 33954879), which suggests that this may be a clinically significant amino acid residue. 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.
GeneDx	RCV001358271	SCV003803308	pathogenic	not provided	2023-02-10	criteria provided, single submitter	clinical testing	In vitro recombination activity assay demonstrated a 22% activity in R764H cells as compared to wild type cells (Kato et al., 2015); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25739914, 26996199, 24290284, 11971977, 27825771)
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001358271	SCV001553960	likely pathogenic	not provided		no assertion criteria provided	clinical testing	The RAG1 p.Arg764His variant was identified in the literature in a boy with an initial diagnosis of selective immunoglobulin A deficiency, however upon analysis of the RAG1 and RAG2 genes was determined to have RAG deficiency. The boy was also carried a deletion of the RAG1 and RAG2 genes, inherited from his healthy father, and a RAG1 p.E455K variant, inherited with the RAG1 p.R764H variant from his healthy mother. Functional analysis of the p.R764H+p.E455K complex allele showed 22.42% RAG1 activity compared to wildtype; whereas the p.R764H and p.E455K variants on their own had 22.42% and 13.73% activity respectively, demonstrating that these alleles have a synergistic effect (Kato_2015_PMID:25739914). The variant was identified in dbSNP (ID: rs768809293) but was not identified in ClinVar and LOVD 3.0. The variant was identified in control databases in 3 of 282738 chromosomes at a frequency of 0.00001061 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 3 of 129084 chromosomes (freq: 0.000023), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other, or South Asian populations. The p.Arg764 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.