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NM_000206.3(IL2RG):c.269G>T (p.Trp90Leu) AND X-linked severe combined immunodeficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 16, 2019
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:
RCV001238084.7

Allele description [Variation Report for NM_000206.3(IL2RG):c.269G>T (p.Trp90Leu)]

NM_000206.3(IL2RG):c.269G>T (p.Trp90Leu)

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.269G>T (p.Trp90Leu)
HGVS:
  • NC_000023.11:g.71110897C>A
  • NG_009088.1:g.5657G>T
  • NG_021141.1:g.892G>T
  • NM_000206.3:c.269G>TMANE SELECT
  • NP_000197.1:p.Trp90Leu
  • LRG_150t1:c.269G>T
  • LRG_150:g.5657G>T
  • NC_000023.10:g.70330747C>A
  • NM_000206.2:c.269G>T
Protein change:
W90L
Links:
dbSNP: rs2092262308
NCBI 1000 Genomes Browser:
rs2092262308
Molecular consequence:
  • NM_000206.3:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001410879Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 16, 2019) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001410879.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with IL2RG-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces tryptophan with leucine at codon 90 of the IL2RG protein (p.Trp90Leu). The tryptophan residue is moderately conserved and there is a small physicochemical difference between tryptophan and leucine. This variant also falls at the last nucleotide of exon 2 of the IL2RG coding sequence, which is part of the consensus splice site for this exon.

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

Last Updated: Sep 29, 2024