Variant: NM_000536.4(RAG2):c.1421A>G (p.Asn474Ser)

CA5950417

496633 (ClinVar)

Gene: RAG2

Condition: recombinase activating gene 2 deficiency

Inheritance Mode: Autosomal recessive inheritance

UUID: feddc439-dbc1-4ed6-b352-a8ce3a5e9e64

Approved on: 2024-01-23

Published on: 2024-01-23

HGVS expressions

NM_000536.4:c.1421A>G
NM_000536.4(RAG2):c.1421A>G (p.Asn474Ser)
NC_000011.10:g.36592748T>C
CM000673.2:g.36592748T>C
NC_000011.9:g.36614298T>C
CM000673.1:g.36614298T>C
NC_000011.8:g.36570874T>C
NG_007573.1:g.10489A>G
NG_033154.1:g.3256T>C
ENST00000311485.8:c.1421A>G
ENST00000311485.7:c.1421A>G
ENST00000524423.1:n.131+5354A>G
ENST00000534663.1:c.*86-219T>C
ENST00000618712.4:c.1421A>G
NM_000536.3:c.1421A>G
NM_001243785.1:c.1421A>G
NM_001243786.1:c.1421A>G
NM_001243785.2:c.1421A>G
NM_001243786.2:c.1421A>G

Uncertain Significance

• Met criteria codes: PM1 PM3_Supporting PP4 PM2_Supporting

• Not Met criteria codes: PS3 PS1 PM5

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 RAG2 Version 1.0.0

Evidence submitted by expert panel

Severe Combined Immunodeficiency Disease VCEP

The c.1421A>G (NM_000536.4) variant in RAG2 is a missense variant predicted to cause substitution of Asparagine by Serine at amino acid 474 (p.Asn474Ser). The filtering allele frequency (the upper threshold of the 95% CI of 2/30614 alleles) of the c.1421A>G variant in RAG2 is 0.00001082 for South Asian chromosomes by gnomAD v2.1.1, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). No homozygotes have been observed in gnomAD. This variant is located in the PHD domain, amino acids 414-487 of RAG2, which is defined as a critical functional domain by the ClinGen SCID VCEP (PMID: 26996199); PM1_Moderate. However, two functional assays published in the literature showed that this variant did not show differences in contrast with wild-type, both in the quantitative assay: The recombination activity assay showed activity of this variant compared to wildtype RAG2 is 97.5% (SEM 5.9), which is higher than the SCID VCEP threshold for Moderate (<25%) or Supporting (25-60%) level of evidence (PMID 29772310) AND in the qualitative assay: The analyses had not yet identified any particular defect associated with the N474S mutation (PMID: 20234091); Thus, PS3 is not applied. Diagnostic criteria for SCID (Criterion 1: Very Low T cells <0.05x109/L + Criterion 3 No alternate explanation for low t-cell count AND <20% of CD4+ T cell have naive cell surface markers - based on CD45RA and CD45R0 count) 0.5pts + T-B-NK+ lymphocyte subset profile 0.5pts, the total is 1 point, PP4 is met (PMID: 11133745). This patient is homozygous, 0.5 pts, PM3 is met at supporting level. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for autosomal recessive recombinase activating gene 2 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PM2_Supporting, PM1_Moderate, PP4, and PM3_Supporting (VCEP specifications version 1.0).

Met criteria codes

• PM1: This variant is located in the PHD domain, amino acids 414-487 of RAG2, which is defined as a critical functional domain by the ClinGen SCID VCEP (PMID: 26996199); PM1_Moderate.
• PM3_Supporting: There is one homozygous patient reported in the literature (PMID: 20234091, 11133745, and 29772310).
• PP4: Diagnostic criteria for SCID (Criterion 1: Very Low T cells <0.05x109/L + Criterion 3 No alternate explanation for low t-cell count AND <20% of CD4+ T cell have naive cell surface markers - based on CD45RA and CD45R0 count) 0.5pts + T-B-NK+ lymphocyte subset profile 0.5pts, the total is 1 point, PP4 is met (PMID: 11133745).
• PM2_Supporting: The filtering allele frequency (the upper threshold of the 95% CI of 2/30614 alleles) of the c.1421A>G variant in RAG2 is 0.00001082 for South Asian chromosomes by gnomAD v2.1.1, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). No homozygotes have been observed in gnomAD.

Not Met criteria codes

• PS3: Two functional assays published in the literature showed that this variant did not show differences in contrast with wild-type, both in the quantitative assay: The recombination activity assay showed activity of this variant compared to wildtype RAG2 is 97.5% (SEM 5.9), which is higher than the SCID VCEP threshold for Moderate (<25%) or Supporting (25-60%) level of evidence (PMID 29772310) AND in the qualitative assay: The analyses had not yet identified any particular defect associated with the N474S mutation (PMID: 20234091); Thus, PS3 is not applied.
• PS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline