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NM_000206.3(IL2RG):c.465G>A (p.Trp155Ter) AND X-linked severe combined immunodeficiency

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 1, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000781480.1

Allele description [Variation Report for NM_000206.3(IL2RG):c.465G>A (p.Trp155Ter)]

NM_000206.3(IL2RG):c.465G>A (p.Trp155Ter)

Gene:
IL2RG:interleukin 2 receptor subunit gamma [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.1
Genomic location:
Preferred name:
NM_000206.3(IL2RG):c.465G>A (p.Trp155Ter)
HGVS:
  • NC_000023.11:g.71110285C>T
  • NG_009088.1:g.6269G>A
  • NG_021141.1:g.1504G>A
  • NM_000206.3:c.465G>AMANE SELECT
  • NP_000197.1:p.Trp155Ter
  • NP_000197.1:p.Trp155Ter
  • LRG_150t1:c.465G>A
  • LRG_150:g.6269G>A
  • LRG_150p1:p.Trp155Ter
  • NC_000023.10:g.70330135C>T
  • NM_000206.2:c.465G>A
Protein change:
W155*
Links:
dbSNP: rs1569479994
NCBI 1000 Genomes Browser:
rs1569479994
Molecular consequence:
  • NM_000206.3:c.465G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
X-linked severe combined immunodeficiency (SCIDX1)
Synonyms:
IMMUNODEFICIENCY 4; X-Linked Combined Immunodeficiency Diseases; Severe combined immunodeficiency, X-linked, T cell-negative, B cell-positive, NK cell-negative; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010315; MedGen: C1279481; Orphanet: 276; OMIM: 300400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000919543Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Feb 1, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919543.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: IL2RG c.465G>A (p.Trp155X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.562C>T [p.Gln188X] and c.703C>T [p.Gln235X]). The variant was absent from 178665 control chromosomes of the gnomAD dataset. To our knowledge, no occurrence of c.465G>A in individuals affected with X-Linked Severe Combined Immunodeficiency and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 29, 2022