rs121918575

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM3PS3_SupportingPP4PM2_SupportingPP1_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

Scores

10
7
2

Clinical Significance

Pathogenic reviewed by expert panel P:10U:1

Conservation

PhyloP100: 7.50
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]
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]

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ACMG classification

Classification made for transcript

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
RAG2NM_000536.4 linkuse as main transcriptc.1352G>C p.Gly451Ala missense_variant 2/2 ENST00000311485.8 NP_000527.2 P55895

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAG2ENST00000311485.8 linkuse as main transcriptc.1352G>C p.Gly451Ala missense_variant 2/21 NM_000536.4 ENSP00000308620.4 P55895

Frequencies

GnomAD3 genomes
AF:
0.0000395
AC:
6
AN:
152038
Hom.:
0
Cov.:
32
show subpopulations
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
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:
0.00
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
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
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
show subpopulations
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:10Uncertain:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityJun 13, 2023- -
Pathogenic, criteria provided, single submitterclinical testingGeneDxOct 27, 2023Published 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 submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2024RAG2: PM3:Very Strong, PM1, PM2, PP3, PS3:Supporting -
Combined immunodeficiency with skin granulomas Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMMay 08, 2008- -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsFeb 29, 2024- -
Recombinase activating gene 2 deficiency Pathogenic:1
Pathogenic, reviewed by expert panelcurationClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGenNov 14, 2023The 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 submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpDec 30, 2020Variant 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 26, 2024This 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 submitterclinical testingFulgent Genetics, Fulgent GeneticsJan 07, 2024- -
Common variable immunodeficiency Pathogenic:1
Pathogenic, criteria provided, single submitterresearchNIHR Bioresource Rare Diseases, University of CambridgeJan 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 submitterresearchPediatric Immunology Service, The Chaim Sheba Medical Center at Tel HaShomerMar 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

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

Other links and lift over

dbSNP: rs121918575; hg19: chr11-36614367; API