11-36592817-C-G

Position:

• chr11-36592817-C-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM3 PS3_Supporting PP4 PM2_Supporting PP1_Strong

This summary comes from the ClinGen Evidence Repository: The NM_000536.4:c.1352G>C variant in RAG2 is a missense variant predicted to cause the substitution of glycine by alanine at amino acid 451 (p.Gly451Ala). The variant has been identified in at least 8 individuals. Three individuals described by Dr. Jolan were homozygous for this variant (reaching the maximum of 1 pt for homozygous occurrence). One individual with Omenn Syndrome was heterozygous for this variant and a p.R229Q variant, which is classified as pathogenic according to the SCID VCEP specifications. The trans phase was not confirmed (0.5 points, PMID 32655540). One individual with CID was heterozygous for this variant, and p.M459L, a likely pathogenic variant classified by the SCID VCEP. The trans phase was not confirmed (0.25pt, PMID 26457731). Three other individuals were heterozygous for this variant and a VUS (p.I210T, PMID 31334206; p.G32E, PMID 26457731; p.T77N, PMID 18463379, 24331380, 26457731, 29772310). 1.75 points in total, PM3 is met.These three homozygous individuals described by Dr. Jolan are from the same family: 3 affected segregations, LOD score 1.81, PP1_Strong. The filtering allele frequency (the upper threshold of the 95% CI of 9/129174 alleles) of this variant in gnomAD v.2.1.1 is 0.00003418 for European (non-Finnish) chromosomes, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting)This variant resides within the PHD domain region, amino acids 414-487, of RAG2, defined as a critical functional domain by the ClinGen SCID VCEP (PM1). In one study (PMID 29772310), a recombination activity assay shows that the relevant activity of the p.G451A variant to wildtype RAG2 is 66.3%, which is higher than the SCID VCEP threshold (<60%) for PS3_supporting. However, in two other studies (PMID 18463379, 24331380), the relevant activity of the variant is shown to be 30% and 27.6%, respectively, which falls in the SCID VCEP threshold (>25% and <60%) for PS3_supporting (PS3_Supporting). Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + SCID gene panel or exome/genome sequencing conducted 0.5pts; the total is 1 point, PP4 is met (PMID:32655540).In summary, this variant meets the criteria to be classified as Pathogenic for SCID due to recombinase activating gene 2 deficiency. ACMG/AMP criteria applied, as specified by the ClinGen SCID-VCEP: PM3, PM2_Supporting, PM1, PS3_Supporting, PP4, and PP1_Strong. (VCEP specifications version 1.0). LINK:https://erepo.genome.network/evrepo/ui/classification/CA122872/MONDO:0000573/124

• Frequency:
  • Genomes: 𝑓 0.000039 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000080 (0 hom.)
• Consequence: RAG2 NM_000536.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:10 U:1
• Conservation: PhyloP100: 7.50

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]

RAG1 (HGNC:9831): (recombination activating 1) The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]

RAG2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 11 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/exons	MANE	Protein	UniProt
RAG2	NM_000536.4	c.1352G>C	p.Gly451Ala	missense_variant	2/2	ENST00000311485.8	NP_000527.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAG2	ENST00000311485.8	c.1352G>C	p.Gly451Ala	missense_variant	2/2	1	NM_000536.4	ENSP00000308620.4

Frequencies

GnomAD3 genomes AF: 0.0000395 AC: 6 AN: 152038 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: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000358 AC: 9 AN: 251488 Hom.: 0 AF XY: 0.0000441 AC XY: 6 AN XY: 135920

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: 0.0000703

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000800 AC: 117 AN: 1461892 Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62 AN XY: 727248

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: 0.000102

Gnomad4 OTH exome AF: 0.0000662

GnomAD4 genome AF: 0.0000395 AC: 6 AN: 152038 Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5 AN XY: 74266

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000793 Hom.: 0

Bravo AF: 0.000110

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.0000412 AC: 5

EpiCase AF: 0.000164

EpiControl AF: 0.000119

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 13, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 27, 2023	Published functional studies demonstrate that the variant has a detrimental effect on V(D)J recombination activity (Schuetz et al., 2008, Tirosh et al., 2019); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24331380, 30877075, 18463379, 26457731, 31334206, 29477728, 29772310, 31388879, 31980526, 21664875, 32655540, 27539235, 26996199, 32581362, 27825771, 20234091) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	RAG2: PM3:Very Strong, PM1, PM2, PP3, PS3:Supporting -

Combined immunodeficiency with skin granulomas Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	May 08, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 29, 2024	- -

Recombinase activating gene 2 deficiency Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen

Nov 14, 2023

The NM_000536.4:c.1352G>C variant in RAG2 is a missense variant predicted to cause the substitution of glycine by alanine at amino acid 451 (p.Gly451Ala). The variant has been identified in at least 8 individuals. Three individuals described by Dr. Jolan were homozygous for this variant (reaching the maximum of 1 pt for homozygous occurrence). One individual with Omenn Syndrome was heterozygous for this variant and a p.R229Q variant, which is classified as pathogenic according to the SCID VCEP specifications. The trans phase was not confirmed (0.5 points, PMID 32655540). One individual with CID was heterozygous for this variant, and p.M459L, a likely pathogenic variant classified by the SCID VCEP. The trans phase was not confirmed (0.25pt, PMID 26457731). Three other individuals were heterozygous for this variant and a VUS (p.I210T, PMID 31334206; p.G32E, PMID 26457731; p.T77N, PMID 18463379, 24331380, 26457731, 29772310). 1.75 points in total, PM3 is met. These three homozygous individuals described by Dr. Jolan are from the same family: 3 affected segregations, LOD score 1.81, PP1_Strong. The filtering allele frequency (the upper threshold of the 95% CI of 9/129174 alleles) of this variant in gnomAD v.2.1.1 is 0.00003418 for European (non-Finnish) chromosomes, which is lower than the ClinGen SCID VCEP threshold (<0.0000588) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting) This variant resides within the PHD domain region, amino acids 414-487, of RAG2, defined as a critical functional domain by the ClinGen SCID VCEP (PM1). In one study (PMID 29772310), a recombination activity assay shows that the relevant activity of the p.G451A variant to wildtype RAG2 is 66.3%, which is higher than the SCID VCEP threshold (<60%) for PS3_supporting. However, in two other studies (PMID 18463379, 24331380), the relevant activity of the variant is shown to be 30% and 27.6%, respectively, which falls in the SCID VCEP threshold (>25% and <60%) for PS3_supporting (PS3_Supporting). Diagnostic criteria for SCID/Leaky SCID/Omenn syndrome met 0.5pts + SCID gene panel or exome/genome sequencing conducted 0.5pts; the total is 1 point, PP4 is met (PMID: 32655540). In summary, this variant meets the criteria to be classified as Pathogenic for SCID due to recombinase activating gene 2 deficiency. ACMG/AMP criteria applied, as specified by the ClinGen SCID-VCEP: PM3, PM2_Supporting, PM1, PS3_Supporting, PP4, and PP1_Strong. (VCEP specifications version 1.0). -

Severe combined immunodeficiency disease Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

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

Dec 30, 2020

Variant summary: RAG2 c.1352G>C (p.Gly451Ala) results in a non-conservative amino acid change located in the Recombination Activating Protein 2, PHD domain (IPR025162) of 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 3.6e-05 in 251488 control chromosomes (gnomAD). c.1352G>C has been reported in the literature in multiple compound heterozygous individuals affected with Combined Immunodeficiency Syndrome (e.g. Scheutz_2008, Walter_2015, Wu_2019). These data indicate that the variant may be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, demonstrating reduced recombination activity or efficiency in cells expressing the variant protein (e.g. Scheutz_2008, Walter_2015, Tirosh_2019). Four other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, citing the variant as pathogenic (n=2) and uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 451 of the RAG2 protein (p.Gly451Ala). This variant is present in population databases (rs121918575, gnomAD 0.008%). This missense change has been observed in individual(s) with ‚ÄãRAG2-related conditions (PMID: 18463379, 26457731, 32581362, 32655540). ClinVar contains an entry for this variant (Variation ID: 13138). 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%. Experimental studies have shown that this missense change affects RAG2 function (PMID: 18463379, 24331380). For these reasons, this variant has been classified 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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jan 07, 2024

- -

Common variable immunodeficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

research

NIHR Bioresource Rare Diseases, University of Cambridge

Jan 01, 2019

- -

Inborn error of immunity;C2673536:Combined immunodeficiency with skin granulomas;CN257931:Recombinase activating gene 2 deficiency Uncertain:1

Uncertain significance, criteria provided, single submitter

research

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

Mar 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.35
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.51
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.63	D;D
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.91	.;D
M_CAP	Uncertain	0.29	D
MetaRNN	Pathogenic	0.91	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.1	M;M
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-1.6	N;.
REVEL	Pathogenic	0.91
Sift	Pathogenic	0.0	D;.
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.96
MVP		0.98
MPC		0.46
ClinPred		0.57	D
GERP RS		5.4
Varity_R		0.67
gMVP		0.74

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: rs121918575; hg19: chr11-36614367;