11-36594065-C-G

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM5_SupportingPP4PS3_ModeratePM2_SupportingPM1_SupportingPM3_Strong

This summary comes from the ClinGen Evidence Repository: The c.104G>C (NM_000536.4) variant in RAG2 is a missense variant predicted to cause the substitution of Glycine by Alanine at amino acid 35 (p.Gly35Ala).The filtering allele frequency (the upper threshold of the 95% CI of 23/1179974 alleles) of the c.104G>C variant in RAG2 is 0.00001295 for European (non-Finnish) chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).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 22.1% (SEM 3.1), which is lower than the SCID VCEP threshold (<25%) for PS3_Moderate, meeting this criterion (PS3_Moderate, PMID 29772310).This variant has been detected in at least 5 individuals with SCID/Leaky SCID/Omenn syndrome in the literature. Of those individuals, one (Proband 35, PMID:30778343) is compound heterozygous for p.K58STer73, which is at least LP according to our specifications. Mother and Father are carriers; the trans phase is confirmed. 1 point. Another proband (Proband 9, PMID:29772310) is a compound heterozygous with E437K, classified as Likely Pathogenic according to SCID VCEP. This patient is being evaluated in the p.Glu437Lys variant curation, so it will not be counted here to avoid circularity. Additionally, 3 individuals were homozygous for the variant (probands 6, 7, and 8, PMID:29772310), reaching the maximum of 1 point for homozygous occurrence; The total is 2 points, PM3_Strong. At least one patient present: * Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5 pts + * Decreased presence of TCRVα7.2 in CD3+ T lymphocytes 0.5 points. The total is 1 point, and then PP4 is met (PMID:29772310). Another missense variant [NM_000536.4(RAG2):c.104G>T (p.Gly35Val)] in the same codon has been reported. The variant was classified as Likely Pathogenic by the ClinGen SCID VCEP (PM5_Supporting).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: PM2_Supporting, PM1_Supporting, PS3_Moderate, PM3_Strong, PP4, PM5_Supporting (VCEP specifications version 1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA214209/MONDO:0000573/124

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

RAG2
NM_000536.4 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:8U:1

Conservation

PhyloP100: 5.85

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 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.

PM5

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 link	c.104G>C	p.Gly35Ala	missense_variant	Exon 2 of 2	ENST00000311485.8	NP_000527.2	P55895

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAG2	ENST00000311485.8 link	c.104G>C	p.Gly35Ala	missense_variant	Exon 2 of 2	1	NM_000536.4	ENSP00000308620.4		P55895

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000655

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

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251316

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135832

show subpopulations

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:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000178

AC:

AN:

1461780

Hom.:

Cov.:

AF XY:

0.0000261

AC XY:

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000198

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152132

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.0000655

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000278

Hom.:

Bravo

AF:

0.0000151

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8Uncertain:1

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Combined immunodeficiency with skin granulomas

Pathogenic:1

Dec 14, 2023

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Recombinase activating gene 2 deficiency

Pathogenic:1

May 13, 2024

ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.104G>C (NM_000536.4) variant in RAG2 is a missense variant predicted to cause the substitution of Glycine by Alanine at amino acid 35 (p.Gly35Ala). The filtering allele frequency (the upper threshold of the 95% CI of 23/1179974 alleles) of the c.104G>C variant in RAG2 is 0.00001295 for European (non-Finnish) chromosomes by gnomAD v4, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). 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 22.1% (SEM 3.1), which is lower than the SCID VCEP threshold (<25%) for PS3_Moderate, meeting this criterion (PS3_Moderate, PMID 29772310). This variant has been detected in at least 5 individuals with SCID/Leaky SCID/Omenn syndrome in the literature. Of those individuals, one (Proband 35, PMID: 30778343) is compound heterozygous for p.K58STer73, which is at least LP according to our specifications. Mother and Father are carriers; the trans phase is confirmed. 1 point. Another proband (Proband 9, PMID: 29772310) is a compound heterozygous with E437K, classified as Likely Pathogenic according to SCID VCEP. This patient is being evaluated in the p.Glu437Lys variant curation, so it will not be counted here to avoid circularity. Additionally, 3 individuals were homozygous for the variant (probands 6, 7, and 8, PMID: 29772310), reaching the maximum of 1 point for homozygous occurrence; The total is 2 points, PM3_Strong. At least one patient present: * Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5 pts + * Decreased presence of TCRVα7.2 in CD3+ T lymphocytes 0.5 points. The total is 1 point, and then PP4 is met (PMID: 29772310). Another missense variant [NM_000536.4(RAG2):c.104G>T (p.Gly35Val)] in the same codon has been reported. The variant was classified as Likely Pathogenic by the ClinGen SCID VCEP (PM5_Supporting). 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: PM2_Supporting, PM1_Supporting, PS3_Moderate, PM3_Strong, PP4, PM5_Supporting (VCEP specifications version 1). -

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

Pathogenic:1

Dec 02, 2022

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS3 supporting, PM2 moderated, PM3 strong, PM5 moderated, PP3 supporting -

Severe combined immunodeficiency disease

Pathogenic:1

Mar 03, 2023

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: RAG2 c.104G>C (p.Gly35Ala) 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 251316 control chromosomes (gnomAD). c.104G>C has been reported in the literature in multiple individuals affected with severe combined immunodeficiency, combined immunodeficiency, hyper IgM syndrome and recurrent infections (examples: Riccetto_2014, Dobbs_2017, Al-Herz_2018, Tirosh_2019, and Alrui_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. Tirosh_2019 have reported recombination activity for this variant (G35A -22%) and G35V was 0.4% as a percentage of wild type, suggesting this residue is critical for the normal function of the protein. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=1) and pathogenic/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided

Pathogenic:1

Jul 08, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The RAG2 c.104G>C; p.Gly35Ala variant (rs148508754, ClinVar Variation ID 36716) is reported in the literature in the compound heterozygous or homozygous state in several individuals affected with severe combined immunodeficiency (SCID), combined immunodeficiency, hyper IgM syndrome, and recurrent infections (Al-Herz 2018, Platt 2021, Riccetto 2014, Tirosh 2019, Walter 2015). This variant is only observed on one allele in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.898), and functional analyses of the variant protein show reduced recombination activity (Schuetz 2023, Tirosh 2019). Additionally, another variant at this codon (c.104G>T; p.Gly35Val) has been reported in the homozygous state in individuals with SCID and is considered pathogenic (Corneo 2001, Meshaal 2019, Platt 2021, Tabori 2004). Based on available information, the p.Gly35Ala variant is considered to be pathogenic. References: Al-Herz W et al. DNA recombination defects in Kuwait: Clinical, immunologic and genetic profile. Clin Immunol. 2018 Feb;187:68-75. PMID: 29051008. Corneo B et al. Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood. 2001 May 1;97(9):2772-6. PMID: 11313270. Meshaal SS et al. Phenotypical heterogeneity in RAG-deficient patients from a highly consanguineous population. Clin Exp Immunol. 2019 Feb;195(2):202-212. PMID: 30307608. Platt CD et al. Efficacy and economics of targeted panel versus whole-exome sequencing in 878 patients with suspected primary immunodeficiency. J Allergy Clin Immunol. 2021 Feb;147(2):723-726. PMID: 32888943. Riccetto AG et al. Compound heterozygous RAG2 mutations mimicking hyper IgM syndrome. J Clin Immunol. 2014 Jan;34(1):7-9. PMID: 24174341. Schuetz C et al. Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT. Blood. 2023 Feb 16;141(7):713-724. PMID: 36279417. Tabori U et al. Detection of RAG mutations and prenatal diagnosis in families presenting with either T-B- severe combined immunodeficiency or Omenn's syndrome. Clin Genet. 2004 Apr;65(4):322-6. PMID: 15025726. Tirosh I et al. Recombination activity of human recombination-activating gene 2 (RAG2) mutations and correlation with clinical phenotype. J Allergy Clin Immunol. 2019 Feb;143(2):726-735. PMID: 29772310. Walter JE et al. Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency. J Clin Invest. 2015 Nov 2;125(11):4135-48. PMID: 26457731. -

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

Pathogenic:1

Sep 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 35 of the RAG2 protein (p.Gly35Ala). This variant is present in population databases (rs148508754, gnomAD 0.003%). This missense change has been observed in individual(s) with severe combined immunodeficiency, combined immunodeficiency, hyper IgM syndrome and recurrent infections (PMID: 24174341, 26457731, 28769923, 29051008, 29772310, 30778343). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 36716). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt RAG2 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects RAG2 function (PMID: 29772310, 31388879). This variant disrupts the p.Gly35 amino acid residue in RAG2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15025726, 30307608). 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. -

RAG2-related disorder

Pathogenic:1

Apr 24, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The RAG2 c.104G>C variant is predicted to result in the amino acid substitution p.Gly35Ala. This variant has been previously reported in the compound heterozygous and homozygous states in individuals with severe combined immunodeficiency (SCID), leaky SCID, or Omenn syndrome (Riccetto et al. 2014. PubMed ID: 24174341; Dobbs et al. 2017. PubMed ID: 28769923; Al-Herz et al. 2018. PubMed ID: 29051008; Aluri et al. 2019. PubMed ID: 30778343; Tirosh et al. 2019. PubMed ID: 29772310). Consistent with these reports, a mutant G35A RAG2 had significantly less activity than wild-type protein in cell-based recombinase activity assays (Tirosh et al. 2019. PubMed ID: 29772310), which suggests the p.Gly35Ala change is deleterious for Rag2 function. A different missense change at the same position, p.Gly35Val, has been reported in multiple unrelated homozygous individuals with RAG2-related disease, and has also been shown in functional studies to abolish recombination activity of the RAG2 protein (Corneo et al. 2000. PubMed ID: 10777560; Tabori et al. 2004. PubMed ID: 15025726; Meshaal et al. 2019. PubMed ID: 30307608; Tirosh et al. 2019. PubMed ID: 29772310). This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as pathogenic. -

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

May 30, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn error of immunity;CN257931:Recombinase activating gene 2 deficiency;na:Atypical severe combined immunodeficiency due to complete RAG1/2 deficiency

Uncertain:1

Mar 06, 2018

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

Significance: Uncertain significance

Review Status: flagged submission

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.80

BayesDel_addAF

Pathogenic

0.31

BayesDel_noAF

Pathogenic

0.31

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.47

T;T;.;.

Eigen

Uncertain

0.65

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Uncertain

0.94

LIST_S2

Pathogenic

0.98

.;D;D;D

M_CAP

Uncertain

0.17

MetaRNN

Pathogenic

0.85

D;D;D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Uncertain

2.3

M;M;.;.

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-1.3

N;.;N;D

REVEL

Pathogenic

0.90

Sift

Pathogenic

0.0

D;.;D;D

Sift4G

Pathogenic

0.0

D;D;.;.

Polyphen

1.0

D;D;.;.

Vest4

0.78

MVP

0.98

MPC

0.45

ClinPred

0.89

GERP RS

5.7

Varity_R

0.53

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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