Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000448.3(RAG1):c.1064T>C (p.Met355Thr)

CA5950092

583401 (ClinVar)

Gene: RAG1

Condition: recombinase activating gene 1 deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 6e78f79c-ace5-4917-b4f4-e3ff31f1a665

Approved on: 2024-02-12

Published on: 2024-02-12

HGVS expressions

NM_000448.3:c.1064T>C

NM_000448.3(RAG1):c.1064T>C (p.Met355Thr)

NC_000011.10:g.36574368T>C

CM000673.2:g.36574368T>C

NC_000011.9:g.36595918T>C

CM000673.1:g.36595918T>C

NC_000011.8:g.36552494T>C

NG_007528.1:g.11356T>C

ENST00000299440.6:c.1064T>C

ENST00000299440.5:c.1064T>C

ENST00000534663.1:c.1064T>C

NM_000448.2:c.1064T>C

NM_001377277.1:c.1064T>C

NM_001377278.1:c.1064T>C

NM_001377279.1:c.1064T>C

NM_001377280.1:c.1064T>C

Uncertain Significance

PM2

Evidence Links 0

Expert Panel

Severe Combined Immunodeficiency Disease VCEP

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAG1 Version 1.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

NM_000448.3(RAG1):c.1064T>C is a missense variant predicted to cause substitution of Methionine by Threonine at amino acid 355 (p.Met355Thr).The highest population minor allele frequency in gnomAD v4 is 0.001815 (11/6062) in Middle Eastern population. (PM2_Supporting, BS1, and BA1 are not met). There are no publications for this variant in the literature. 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: No criteria met (VCEP specifications version 1).

PM2

The highest population minor allele frequency in gnomAD v4 is 0.001815 (11/6062) in Middle Eastern population. (PM2_Supporting, BS1, and BA1 are not met)

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