NM_002185.5(IL7R):c.156_157delinsTT (p.Gln52_His53delinsHisTyr) AND Immunodeficiency 104

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 7, 2022
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:: RCV000793702.4

Allele description [Variation Report for NM_002185.5(IL7R):c.156_157delinsTT (p.Gln52_His53delinsHisTyr)]

NM_002185.5(IL7R):c.156_157delinsTT (p.Gln52_His53delinsHisTyr)

Gene:

IL7R:interleukin 7 receptor [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_002185.5(IL7R):c.156_157delinsTT (p.Gln52_His53delinsHisTyr)

HGVS:

NC_000005.10:g.35860925_35860926delinsTT
NG_009567.1:g.9037_9038delinsTT
NM_002185.2:c.156_157delinsTT
NM_002185.5:c.156_157delinsTTMANE SELECT
NP_002176.2:p.Gln52_His53delinsHisTyr
LRG_74t1:c.156_157delinsTT
LRG_74:g.9037_9038delinsTT
NC_000005.9:g.35861027_35861028delinsTT
NM_002185.3:c.156_157delGCinsTT
NR_120485.3:n.243_244delinsTT

Links:

dbSNP: rs1580851810

NCBI 1000 Genomes Browser:

rs1580851810

Molecular consequence:

NM_002185.5:c.156_157delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NR_120485.3:n.243_244delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Immunodeficiency 104
Synonyms:: SCID, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive; IMMUNODEFICIENCY 104, SEVERE COMBINED; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012163; MedGen: C5676890; OMIM: 608971

Recent activity

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phosphatidylinositol 3-kinase regulatory subunit gamma isoform X1 [Paramormyrops...
phosphatidylinositol 3-kinase regulatory subunit gamma isoform X1 [Paramormyrops kingsleyae]
gi|1338815873|ref|XP_023650305.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000933068	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 7, 2022)	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

SCV000933068

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 7, 2022)

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, SCV000933068.3

#	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.156_157delinsTT, is a complex sequence change that results in the deletion of 2 and insertion of 2 amino acid(s) in the IL7R protein (p.Gln52_His53delinsHisTyr). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with IL7R-related conditions. ClinVar contains an entry for this variant (Variation ID: 640639). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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