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NM_000448.3(RAG1):c.303G>A (p.Ala101=) AND Recombinase activating gene 1 deficiency

Germline classification:
Benign (1 submission)
Last evaluated:
Nov 14, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003398749.1

Allele description [Variation Report for NM_000448.3(RAG1):c.303G>A (p.Ala101=)]

NM_000448.3(RAG1):c.303G>A (p.Ala101=)

Gene:
RAG1:recombination activating 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p12
Genomic location:
Preferred name:
NM_000448.3(RAG1):c.303G>A (p.Ala101=)
Other names:
p.A101A:GCG>GCA; NM_000448.3(RAG1):c.303G>A; p.Ala101=
HGVS:
  • NC_000011.10:g.36573607G>A
  • NG_007528.1:g.10595G>A
  • NM_000448.3:c.303G>AMANE SELECT
  • NM_001377277.1:c.303G>A
  • NM_001377278.1:c.303G>A
  • NM_001377279.1:c.303G>A
  • NM_001377280.1:c.303G>A
  • NP_000439.1:p.Ala101=
  • NP_000439.2:p.Ala101=
  • NP_001364206.1:p.Ala101=
  • NP_001364207.1:p.Ala101=
  • NP_001364208.1:p.Ala101=
  • NP_001364209.1:p.Ala101=
  • LRG_98t1:c.303G>A
  • LRG_98:g.10595G>A
  • LRG_98p1:p.Ala101=
  • NC_000011.9:g.36595157G>A
  • NM_000448.2:c.303G>A
Links:
dbSNP: rs4151025
NCBI 1000 Genomes Browser:
rs4151025
Molecular consequence:
  • NM_000448.3:c.303G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001377277.1:c.303G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001377278.1:c.303G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001377279.1:c.303G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001377280.1:c.303G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Recombinase activating gene 1 deficiency
Identifiers:
MONDO: MONDO:0000572; MedGen: CN375631

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004102808ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen SCID ACMG Specifications RAG1 V1.0.0)		Benign
(Nov 14, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen, SCV004102808.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.303G>A (p.Ala101=) variant (NM_000022.4) is a synonymous (silent) variant that is not predicted by SpliceAI and varSEAK to impact splicing (BP7). The filtering allele frequency (the lower threshold of the 95% CI of 799/30614) of the c.303G>A variant in RAG1 is 0.02460 for South Asian chromosomes by gnomAD v2.1.1 which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1 and therefore meets this criterion (BA1). Additionally, 76 homozygous individuals were reported (BS2_Supporting is met). In summary, this variant is classified as a Benign for autosomal recessive SCID based on ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP (specification version 1.0): BA1, BS2_Supporting, and BP7.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025