Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!

Variant: NM_000536.4(RAG2):c.14T>A (p.Met5Lys)

CA5950635

304560 (ClinVar)

Gene: RAG2
Condition: recombinase activating gene 2 deficiency
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 2d3d6a0f-a123-4931-a57e-01aed2248bb2
Approved on: 2024-05-01
Published on: 2024-05-01

HGVS expressions

NM_000536.4:c.14T>A
NM_000536.4(RAG2):c.14T>A (p.Met5Lys)
NC_000011.10:g.36594155A>T
CM000673.2:g.36594155A>T
NC_000011.9:g.36615705A>T
CM000673.1:g.36615705A>T
NC_000011.8:g.36572281A>T
NG_007573.1:g.9082T>A
NG_033154.1:g.4663A>T
ENST00000527033.6:c.14T>A
ENST00000529083.2:c.14T>A
ENST00000532616.2:c.14T>A
ENST00000311485.8:c.14T>A
ENST00000311485.7:c.14T>A
ENST00000524423.1:n.131+3947T>A
ENST00000527033.5:c.14T>A
ENST00000529083.1:c.14T>A
ENST00000618712.4:c.14T>A
NM_000536.3:c.14T>A
NM_001243785.1:c.14T>A
NM_001243786.1:c.14T>A
NM_001243785.2:c.14T>A
NM_001243786.2:c.14T>A
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Uncertain Significance

Met criteria codes 1
PM1_Supporting
Not Met criteria codes 1
PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAG2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
NM_000536.4(RAG2):c.14T>A is a missense variant predicted to cause substitution of Methionine by Lysine at amino acid 5 (p.Met5Lys). This missense variant is located in the core domain (amino acids 1-383) (PM1_supporting).The highest population minor allele frequency in gnomAD v4 is 0.0003307 (389/1176246) in European (non-Finnish) population (PM2_Supporting, BS1, and BA1 are not met). To our knowledge, this variant has not been reported in the literature in individuals affected with RAG2 related conditions or in functional studies. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for autosomal recessive severe combined immunodeficiency due to RAG2 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PM1_supporting (VCEP specifications version 1).
Met criteria codes
PM1_Supporting
This missense variant is located in the core domain (amino acids 1-383) (PM1_supporting).
Not Met criteria codes
PM2
The highest population minor allele frequency in gnomAD v4 is 0.0003307 (389/1176246) in European (non-Finnish) population. (PM2_Supporting, BS1, and BA1 are not met)
Curation History
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