11-36593976-C-A

Position:

• chr11-36593976-C-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1_Supporting PM3_Supporting PP4 PS3_Moderate PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000536.4:c.193G>T variant in RAG2 is a missense variant predicted to cause substitution of aspartic acid by tyrosine at amino acid 65 (p.Asp74Tyr). The variant has been reported in one individual with SCID. The individual was homozygous of this variant (PM3_Supporting, PMID 21624848). The individual had a T-B-NK+ lymphocyte profile and showed reduced T-cell proliferation under PHA stimulation, which supports a diagnosis of leaky/atypical SCID (PP4, PMID 21624848). The highest population minor allele frequency of this variant in gnomAD v2.1.1 is 0.000008791 (1/113758 alleles) in the European (non-Finnish) population, which is lower than the SCID-VCEP threshold (<0.0000588) for PM2_Supporting. No homozygous individual has been observed in the gnomAD v2.1.1 (PM2_Supporting). This variant resides within the core domain (amino acids 1-383) of RAG2, defined as a critical functional domain by the ClinGen SCID VCEP. (PM1_Supporting). An in vitro recombination activity assay shows that the relevant activity of the p.D65Y variant compared to wildtype RAG2 is 6.8%, which is below the threshold (<25%) established by the SCID VCEP for PS3_Moderate (PS3_Moderate, PMID 29772310). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive recombinase activating gene 2 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PP4, PM3_Supporting, PM2_Supporting, PM1_Supporting, and PS3_Moderate (VCEP specifications version 1.0). LINK:https://erepo.genome.network/evrepo/ui/classification/CA380144219/MONDO:0000573/124

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: RAG2 NM_000536.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:5 U:1
• Conservation: PhyloP100: 5.61

Genes affected

RAG2 (HGNC:9832): (recombination activating 2) This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The recombination activating gene 1 component is thought to contain most of the catalytic activity, while the N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components, specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a form of severe combined immunodeficiency associated with autoimmune-like symptoms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAG2	NM_000536.4	c.193G>T	p.Asp65Tyr	missense_variant	2/2	ENST00000311485.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAG2	ENST00000311485.8	c.193G>T	p.Asp65Tyr	missense_variant	2/2	1	NM_000536.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251474 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135914

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461886 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Recombinase activating gene 2 deficiency Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen

Nov 14, 2023

The NM_000536.4:c.193G>T variant in RAG2 is a missense variant predicted to cause substitution of aspartic acid by tyrosine at amino acid 65 (p.Asp74Tyr). The variant has been reported in one individual with SCID. The individual was homozygous of this variant (PM3_Supporting, PMID 21624848). The individual had a T-B-NK+ lymphocyte profile and showed reduced T-cell proliferation under PHA stimulation, which supports a diagnosis of leaky/atypical SCID (PP4, PMID 21624848). The highest population minor allele frequency of this variant in gnomAD v2.1.1 is 0.000008791 (1/113758 alleles) in the European (non-Finnish) population, which is lower than the SCID-VCEP threshold (<0.0000588) for PM2_Supporting. No homozygous individual has been observed in the gnomAD v2.1.1 (PM2_Supporting). This variant resides within the core domain (amino acids 1-383) of RAG2, defined as a critical functional domain by the ClinGen SCID VCEP. (PM1_Supporting). An in vitro recombination activity assay shows that the relevant activity of the p.D65Y variant compared to wildtype RAG2 is 6.8%, which is below the threshold (<25%) established by the SCID VCEP for PS3_Moderate (PS3_Moderate, PMID 29772310). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive recombinase activating gene 2 deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PP4, PM3_Supporting, PM2_Supporting, PM1_Supporting, and PS3_Moderate (VCEP specifications version 1.0). -

Inborn error of immunity;C1832322:Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;CN257931:Recombinase activating gene 2 deficiency Pathogenic:1

Likely pathogenic, criteria provided, single submitter

research

Pediatric Immunology Service, The Chaim Sheba Medical Center at Tel HaShomer

Mar 06, 2018

- -

Severe combined immunodeficiency disease Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 14, 2023

Variant summary: RAG2 c.193G>T (p.Asp65Tyr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251474 control chromosomes (gnomAD). c.193G>T has been reported in the literature in an individual homozygous for the variant affected with Severe Combined Immunodeficiency (Dalal_2011). These data indicate that the variant may be associated with disease. At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated severely decreased recombinase activity (Tirosh_2019). Four submitters have provided clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic (n=1), likely pathogenic (n=2), or uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jan 20, 2020

Published functional studies demonstrate a damaging effect with a recombination activity of 6.8% of WT hRAG2(Tirosh 2018); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21624848, 29772310) -

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;C2673536:Combined immunodeficiency with skin granulomas;C2700553:Histiocytic medullary reticulosis Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Nov 12, 2021

- -

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;C2673536:Combined immunodeficiency with skin granulomas Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Dec 28, 2021

This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 65 of the RAG2 protein (p.Asp65Tyr). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This missense change has been observed in individual(s) with severe combined immunodeficiency (PMID: 21624848). ClinVar contains an entry for this variant (Variation ID: 427020). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RAG2 protein function. Experimental studies have shown that this missense change affects RAG2 function (PMID: 29772310). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.41
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.87	D;D;.;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.99	.;D;D;D
M_CAP	Uncertain	0.13	D
MetaRNN	Pathogenic	0.92	D;D;D;D
MetaSVM	Pathogenic	0.96	D
MutationAssessor	Pathogenic	3.1	M;M;.;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.57	T
PROVEAN	Pathogenic	-4.9	D;.;D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;.;D;D
Sift4G	Pathogenic	0.0	D;D;.;.
Polyphen		1.0	D;D;.;.
Vest4		0.86
MutPred		0.79		Loss of phosphorylation at Y68 (P = 0.0727);Loss of phosphorylation at Y68 (P = 0.0727);Loss of phosphorylation at Y68 (P = 0.0727);Loss of phosphorylation at Y68 (P = 0.0727);
MVP		0.96
MPC		0.49
ClinPred		0.99	D
GERP RS		5.8
Varity_R		0.78
gMVP		0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs909264507; hg19: chr11-36615526;