rs765298019

Variant names:

• chr11-36593484-G-A
• rs765298019
• NM_000536.4:c.685C>T

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PS3_Moderate PM2_Supporting PM3_Strong PM1_Supporting PP1 PP4

This summary comes from the ClinGen Evidence Repository: The c.685C>T (NM_000536.4) variant in RAG2 is a missense variant predicted to cause the substitution of Arginine by Tryptophan at amino acid 229 (p.Arg229Trp).The filtering allele frequency (the upper threshold of the 95% CI of (11/1180024 alleles) is 0.000005000 in gnomad v4 for the European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, meeting this criterion (PM2_Supporting). No homozygous has been described.This variant is located in the core domain, amino acids 1-383 of RAG2, which is defined as a critical functional domain by the ClinGen SCID VCEP (PMID:26996199); PM1_Supporting.The recombination activity assay showed activity of this variant compared to wildtype RAG2 is 10.5% (SEM 0.5), which is lower than the SCID VCEP threshold (<25%) for PS3_Moderate, meeting this criterion (PS3_Moderate, PMID 29772310).The variant has been reported to segregate in two affected family members (Proband + 1) (PP1); (Proband 30a and 30b, PMID:11133745).At least 9 probands were reported in the literature carrying this variant. 8 of them were homozygous, reaching the maximum of 1 point for homozygous occurrence. Also, 1 proband is compound heterozygous for paternal Arg229Trp and maternal Gly95Arg, which is likely pathogenic according to SCID VCEP specifications, as phase is confirmed; 1 point—a total of 2 points, PM3_Strong.Proband 24 presents: *Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + *T-B-NK+ lymphocyte subset profile 0.5pts; total 1pt, PP4 is met (PMID:11133745).In summary, this variant meets the criteria to be classified as 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: PM2_Supporting, PM1_Supporting, PS3_Moderate, PP1, PM3_Strong, and PP4 (VCEP specifications version 1.0). LINK:https://erepo.genome.network/evrepo/ui/classification/CA5950542/MONDO:0000573/124

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000089 (0 hom.)
• Consequence: RAG2 NM_000536.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5 U:1
• Conservation: PhyloP100: 3.67
• Publications: 13 publications found

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]

RAG2 Gene-Disease associations (from GenCC):

• Omenn syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, G2P, Orphanet
• recombinase activating gene 2 deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAG2	NM_000536.4	c.685C>T	p.Arg229Trp	missense_variant	Exon 2 of 2	ENST00000311485.8	NP_000527.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAG2	ENST00000311485.8	c.685C>T	p.Arg229Trp	missense_variant	Exon 2 of 2	1	NM_000536.4	ENSP00000308620.4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152128 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251144 AF XY: 0.00000737

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 FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000889 AC: 13 AN: 1461720 Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6 AN XY: 727180

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53254

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000899 AC: 10 AN: 1112004

Other (OTH) AF: 0.0000166 AC: 1 AN: 60396

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152128 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74298

African (AFR) AF: 0.00 AC: 0 AN: 41422

American (AMR) AF: 0.00 AC: 0 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68020

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.0000272 Hom.: 0

Bravo AF: 0.0000151

ExAC AF: 0.00000824 AC: 1

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Combined immunodeficiency with skin granulomas Pathogenic:1

Apr 18, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Recombinase activating gene 2 deficiency Pathogenic:1

Apr 01, 2024

ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.685C>T (NM_000536.4) variant in RAG2 is a missense variant predicted to cause the substitution of Arginine by Tryptophan at amino acid 229 (p.Arg229Trp). The filtering allele frequency (the upper threshold of the 95% CI of (11/1180024 alleles) is 0.000005000 in gnomad v4 for the European (non-Finnish) population, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, meeting this criterion (PM2_Supporting). No homozygous has been described. This variant is located in the core domain, amino acids 1-383 of RAG2, which is defined as a critical functional domain by the ClinGen SCID VCEP (PMID: 26996199); PM1_Supporting. The recombination activity assay showed activity of this variant compared to wildtype RAG2 is 10.5% (SEM 0.5), which is lower than the SCID VCEP threshold (<25%) for PS3_Moderate, meeting this criterion (PS3_Moderate, PMID 29772310). The variant has been reported to segregate in two affected family members (Proband + 1) (PP1); (Proband 30a and 30b, PMID: 11133745). At least 9 probands were reported in the literature carrying this variant. 8 of them were homozygous, reaching the maximum of 1 point for homozygous occurrence. Also, 1 proband is compound heterozygous for paternal Arg229Trp and maternal Gly95Arg, which is likely pathogenic according to SCID VCEP specifications, as phase is confirmed; 1 point—a total of 2 points, PM3_Strong. Proband 24 presents: *Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + *T-B-NK+ lymphocyte subset profile 0.5pts; total 1pt, PP4 is met (PMID: 11133745). In summary, this variant meets the criteria to be classified as 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: PM2_Supporting, PM1_Supporting, PS3_Moderate, PP1, PM3_Strong, and PP4 (VCEP specifications version 1.0). -

Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive Pathogenic:1

Dec 02, 2023

Laboratory of Hereditary Immune Disorders, Research Centre for Medical Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The missense variant NM_000536.4(RAG2):c.685C>T, p.(Arg229Trp) was identified in a homozygous state in a proband diagnosed with SCID in Russian pilot NBS project covering more than 200,000 newborns. This variant has been previously reported in the literature multiple times (PMIDs: 11133745, 15025726, 21625022, 34664192) and is listed in gnomAD v2.1.1 once in heterozygous individuals. The affected amino acid position is evolutionarily conserved, and multiple in silico prediction tools support a deleterious effect. Furthermore, functional studies have demonstrated a damaging impact on recombination activity (PMID: 29772310). Taken together, the variant meets the following ACMG/AMP criteria and can be classified as pathogenic with PM2, PP3, PS1, PS3, PP5, PP4 criteria. -

Histiocytic medullary reticulosis Pathogenic:1

Sep 16, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

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

Feb 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 229 of the RAG2 protein (p.Arg229Trp). This variant is present in population databases (rs765298019, gnomAD 0.002%). This missense change has been observed in individuals with RAG2-related disease (PMID: 11133745, 15025726, 16960852, 28747913). ClinVar contains an entry for this variant (Variation ID: 496624). 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 with a positive predictive value of 95%. This variant disrupts the p.Arg229 amino acid residue in RAG2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11133745, 24144642, 26915675). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Inborn error of immunity;C1832322:Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive;C2700553:Histiocytic medullary reticulosis;CN257931:Recombinase activating gene 2 deficiency Uncertain:1

Mar 06, 2018

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.47
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D;D
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Pathogenic	1.0	.;D
M_CAP	Uncertain	0.19	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	H;H
PhyloP100		3.7
PrimateAI	Uncertain	0.53	T
PROVEAN	Pathogenic	-7.5	D;.
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D;.
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.85
MutPred		0.97		Gain of catalytic residue at R229 (P = 0.0891);Gain of catalytic residue at R229 (P = 0.0891);
MVP		0.99
MPC		0.45
ClinPred		1.0	D
GERP RS		4.7
Varity_R		0.84
gMVP		0.90
Mutation Taster		=11/89	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs765298019; hg19: chr11-36615034;