NM_000206.3(IL2RG):c.431_433delinsGGG (p.Gln144_Met145delinsArgVal) AND X-linked severe combined immunodeficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 29, 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:: RCV003511073.2

Allele description [Variation Report for NM_000206.3(IL2RG):c.431_433delinsGGG (p.Gln144_Met145delinsArgVal)]

NM_000206.3(IL2RG):c.431_433delinsGGG (p.Gln144_Met145delinsArgVal)

Gene:

IL2RG:interleukin 2 receptor subunit gamma [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

Xq13.1

Genomic location:

Preferred name:

NM_000206.3(IL2RG):c.431_433delinsGGG (p.Gln144_Met145delinsArgVal)

HGVS:

NC_000023.11:g.71110525_71110527delinsCCC
NG_009088.1:g.6027_6029delinsGGG
NG_021141.1:g.1262_1264delinsGGG
NM_000206.3:c.431_433delinsGGGMANE SELECT
NP_000197.1:p.Gln144_Met145delinsArgVal
NP_000197.1:p.Gln144_Met145delinsArgVal
LRG_150t1:c.431_433delinsGGG
LRG_150:g.6027_6029delinsGGG
LRG_150p1:p.Gln144_Met145delinsArgVal
NC_000023.10:g.70330375_70330377delinsCCC
NM_000206.2:c.431_433delinsGGG

Links:

dbSNP: rs1602289405

NCBI 1000 Genomes Browser:

rs1602289405

Molecular consequence:

NM_000206.3:c.431_433delinsGGG - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004276646	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 29, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004276646

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 29, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004276646.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.431_433delinsGGG, is a complex sequence change that results in the replacement of 2 amino acids of the IL2RG protein (p.Gln144_Met145delinsArgVal). 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. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant has not been reported in the literature in individuals with IL2RG-related disease. This variant is not present in population databases (ExAC no frequency).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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