rs869320659

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS4PM1_StrongPS3_SupportingPM6PP4PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000206.3(IL2RG):c.676C>T (p.Arg226Cys) missense variant resides within a CpG dinucleotide region, cDNA 676-677 encoding amino acid R226, of IL2RG that is defined as a mutational hotspot (PMID:7668284; PM1_Strong). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The male (0.5pt) patient of PMID:14966353 has a T-B+NK- lymphocyte subset profile (0.5pt) [CD3: 2.5%; CD19: 95.4%; CD16/CD56: 0.5%] which is specific for SCID due to gamma chain deficiency (1pt; PP4). In a second case, the R226C variant arose de novo as a somatic mutation early in embryogenesis in the mother of the patient, 1 pt, PM6_Moderate (PMID:23683512).At least eight additional male X-SCID patients have been reported (PMIDs: 9058718, 11129345, 22936741, 7668284) with this hemizygous variant (total 4.5pt; PS4). PMID:7632950 Examined the mutant 7 chain distribution by confocal microscopy in transiently transfected COS-7 cells, comparing it with the wild-type 7 chain distribution. The mutant 7 chain could not be detected by an antihuman IL-2 receptor 7 chain monoclonal antibody, TUGh4, on the cell surface of the transfected COS-7 cells. This result was in sharp contrast to that obtained with the wild-type γ chain, which was clearly stained by TUGh4 on the transfected cells. PS3_Supporting is met.In summary, this variant meets the criteria to be classified as Pathogenic for X-linked T-B+ severe combined immunodeficiency due to gamma chain deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PS4, PM1_Strong, PM6_Moderate, PM2_Supporting, PS3_Supporting, and PP4. (VCEP specifications version 1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA358784/MONDO:0010315/129

Frequency

Genomes: not found (cov: 23)

Consequence

IL2RG
ENST00000374202.7 missense

Scores

11
5
1

Clinical Significance

Pathogenic reviewed by expert panel P:8

Conservation

PhyloP100: 3.56
Variant links:
Genes affected
IL2RG (HGNC:6010): (interleukin 2 receptor subunit gamma) The protein encoded by this gene is an important signaling component of many interleukin receptors, including those of interleukin -2, -4, -7 and -21, and is thus referred to as the common gamma chain. Mutations in this gene cause X-linked severe combined immunodeficiency (XSCID), as well as X-linked combined immunodeficiency (XCID), a less severe immunodeficiency disorder. [provided by RefSeq, Mar 2010]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 13 ACMG points.

PS3
For more information check the summary or visit ClinGen Evidence Repository.
PS4
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.
PM6
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
IL2RGNM_000206.3 linkuse as main transcriptc.676C>T p.Arg226Cys missense_variant 5/8 ENST00000374202.7 NP_000197.1
IL2RGXM_047442089.1 linkuse as main transcriptc.676C>T p.Arg226Cys missense_variant 5/7 XP_047298045.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL2RGENST00000374202.7 linkuse as main transcriptc.676C>T p.Arg226Cys missense_variant 5/81 NM_000206.3 ENSP00000363318 P1P31785-1

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:8
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

X-linked severe combined immunodeficiency Pathogenic:4
Pathogenic, no assertion criteria providedclinical testingCounsylMar 12, 2018- -
Pathogenic, reviewed by expert panelcurationClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGenNov 14, 2023The NM_000206.3(IL2RG):c.676C>T (p.Arg226Cys) missense variant resides within a CpG dinucleotide region, cDNA 676-677 encoding amino acid R226, of IL2RG that is defined as a mutational hotspot (PMID: 7668284; PM1_Strong). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The male (0.5pt) patient of PMID: 14966353 has a T-B+NK- lymphocyte subset profile (0.5pt) [CD3: 2.5%; CD19: 95.4%; CD16/CD56: 0.5%] which is specific for SCID due to gamma chain deficiency (1pt; PP4). In a second case, the R226C variant arose de novo as a somatic mutation early in embryogenesis in the mother of the patient, 1 pt, PM6_Moderate (PMID: 23683512). At least eight additional male X-SCID patients have been reported (PMIDs: 9058718, 11129345, 22936741, 7668284) with this hemizygous variant (total 4.5pt; PS4). PMID: 7632950 Examined the mutant 7 chain distribution by confocal microscopy in transiently transfected COS-7 cells, comparing it with the wild-type 7 chain distribution. The mutant 7 chain could not be detected by an antihuman IL-2 receptor 7 chain monoclonal antibody, TUGh4, on the cell surface of the transfected COS-7 cells. This result was in sharp contrast to that obtained with the wild-type γ chain, which was clearly stained by TUGh4 on the transfected cells. PS3_Supporting is met. In summary, this variant meets the criteria to be classified as Pathogenic for X-linked T-B+ severe combined immunodeficiency due to gamma chain deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PS4, PM1_Strong, PM6_Moderate, PM2_Supporting, PS3_Supporting, and PP4. (VCEP specifications version 1). -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 16, 2023Advanced 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 IL2RG protein function. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 225195). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 226 of the IL2RG protein (p.Arg226Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with SCID (PMID: 7668284, 9058718, 14966353, 22039266, 23683512). In at least one individual the variant was observed to be de novo. -
Pathogenic, criteria provided, single submitterclinical testingNeuberg Centre For Genomic Medicine, NCGMJun 22, 2023The observed missense variant c.676C>T(p.Arg226Cys) in IL2RG gene has been reported previously in individual(s) with SCID. A different missense variant [c.677G>A; p.Arg226His] at the same position has been previously reported as pathogenic (Recher M, et al, 2011; Dong W, et al., 2023). Functional characterization of the variant indicate that the p.Arg226Cys substitution (referred to as p.Arg204Cys in the literature) results in the lack of cell surface expression of the IL2 receptor gamma chain (Kumaki S, et al., 1995). This variant is absent in the gnomAD Exomes. This variant has been reported to the ClinVar database as Pathogenic. The amino acid Arg at position 226 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen - Possibly damaging, SIFT – Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. The residue is conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
X-linked severe combined immunodeficiency;CN030319:Combined immunodeficiency, X-linked Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingJuno Genomics, Hangzhou Juno Genomics, Inc-PM2_Supporting+PM5+PS3_Supporting+PS4+PM6_Supporting+PP4 -
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsOct 31, 2018- -
Combined immunodeficiency, X-linked Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingRady Children's Institute for Genomic Medicine, Rady Children's Hospital San DiegoNov 21, 2018The c.676C>T, p.Arg226Cys has previously been reported in the literature as pathogenic (PMID: 7668284, 23683512) and by clinical laboratories in ClinVar as associated with X-linked SCID. Missense variants at the same codon (R226H) have also been identified in patients with SCID (PMID: 7668284). Functional characterization of the variant indicate that the p.Arg226Cys substitution (referred to as p.Arg204Cys in the literature) results in the lack of cell surface expression of the IL2 receptor gamma chain (PMID: 7632950). There are no reports of the variant in the population allele frequency database, gnomAD, thus the variant is presumed rare. The variant results in a non-conservative amino acid change at a conserved residue, and in silico protein models predict a damaging effect on protein function. Based on the combined evidence, this variant is classified as pathogenic. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingGeneDxMar 15, 2023Published functional studies demonstrate variant impairs expression of the IL2RG protein (Kumaki et al., 1995); Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8299698, 8956936, 10444186, 32265911, 30778343, 7668284, 7632950, 9058718, 9921912, 11213805, 22832027, 28780374, 23683512, 30273710, 14966353, 32888943, 36007526, 35874699, 9399950) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.58
BayesDel_addAF
Pathogenic
0.61
D
BayesDel_noAF
Pathogenic
0.64
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.94
D;.;.
FATHMM_MKL
Uncertain
0.80
D
LIST_S2
Uncertain
0.94
D;D;D
M_CAP
Pathogenic
0.79
D
MetaRNN
Pathogenic
0.98
D;D;D
MetaSVM
Pathogenic
0.96
D
MutationAssessor
Uncertain
2.4
M;.;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.61
T
PROVEAN
Pathogenic
-6.1
D;D;D
REVEL
Pathogenic
0.73
Sift
Uncertain
0.0010
D;D;D
Sift4G
Pathogenic
0.0010
D;D;.
Polyphen
1.0
D;.;.
Vest4
0.60
MutPred
0.91
Loss of MoRF binding (P = 0.0065);.;.;
MVP
1.0
MPC
1.8
ClinPred
1.0
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.70
gMVP
0.87

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: rs869320659; hg19: chrX-70329159; API