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NM_000536.4(RAG2):c.1492A>T (p.Lys498Ter) AND RAG2-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 28, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003918788.2

Allele description [Variation Report for NM_000536.4(RAG2):c.1492A>T (p.Lys498Ter)]

NM_000536.4(RAG2):c.1492A>T (p.Lys498Ter)

Gene:
RAG2:recombination activating 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p12
Genomic location:
Preferred name:
NM_000536.4(RAG2):c.1492A>T (p.Lys498Ter)
HGVS:
  • NC_000011.10:g.36592677T>A
  • NG_007573.1:g.10560A>T
  • NG_033154.1:g.3185T>A
  • NM_000536.4:c.1492A>TMANE SELECT
  • NM_001243785.2:c.1492A>T
  • NM_001243786.2:c.1492A>T
  • NP_000527.2:p.Lys498Ter
  • NP_001230714.1:p.Lys498Ter
  • NP_001230715.1:p.Lys498Ter
  • LRG_99:g.10560A>T
  • NC_000011.9:g.36614227T>A
  • NC_000011.9:g.36614227T>A
  • NM_000536.3:c.1492A>T
Protein change:
K498*
Links:
dbSNP: rs373151027
NCBI 1000 Genomes Browser:
rs373151027
Molecular consequence:
  • NM_000536.4:c.1492A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001243785.2:c.1492A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001243786.2:c.1492A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
RAG2-related disorder
Synonyms:
RAG2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004729978PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Nov 28, 2023) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004729978.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The RAG2 c.1492A>T variant is predicted to result in premature protein termination (p.Lys498*). This variant has been reported in the heterozygous state in one individual in a carrier study (Table S9, Reported as genomic position 36570803, Bell et al. 2011. PubMed ID: 21228398). This variant is reported in 0.012% of alleles in individuals of Latino descent in gnomAD. Nonsense variants in RAG2 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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

Last Updated: Oct 13, 2024