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NM_001290043.2(TAP2):c.773C>T (p.Thr258Ile) AND MHC class I deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 20, 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:
RCV002599939.3

Allele description [Variation Report for NM_001290043.2(TAP2):c.773C>T (p.Thr258Ile)]

NM_001290043.2(TAP2):c.773C>T (p.Thr258Ile)

Gene:
TAP2:transporter 2, ATP binding cassette subfamily B member [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NM_001290043.2(TAP2):c.773C>T (p.Thr258Ile)
HGVS:
  • NC_000006.12:g.32835326G>A
  • NG_009793.4:g.8445C>T
  • NM_000544.3:c.773C>T
  • NM_001290043.2:c.773C>TMANE SELECT
  • NM_018833.3:c.773C>T
  • NP_000535.3:p.Thr258Ile
  • NP_001276972.1:p.Thr258Ile
  • NP_061313.2:p.Thr258Ile
  • LRG_167t1:c.773C>T
  • LRG_167t2:c.773C>T
  • LRG_167:g.8445C>T
  • LRG_167p1:p.Thr258Ile
  • LRG_167p2:p.Thr258Ile
  • NC_000006.11:g.32803103G>A
Protein change:
T258I
Molecular consequence:
  • NM_000544.3:c.773C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290043.2:c.773C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018833.3:c.773C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
MHC class I deficiency
Synonyms:
BARE LYMPHOCYTE SYNDROME, TYPE I; BLS, TYPE I
Identifiers:
MONDO: MONDO:0011476; MedGen: C1858266; Orphanet: 34592; OMIM: PS604571

Recent activity

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  • Chain F, CS2it1p2_F7K Fab heavy chain
    Chain F, CS2it1p2_F7K Fab heavy chain
    gi|2559884529|pdb|8TCO|F
    Protein
  • Dysentery, Amebic
    Dysentery, Amebic
    DYSENTERY caused by intestinal amebic infection, chiefly with ENTAMOEBA HISTOLYTICA. This condition may be associated with amebic infection of the LIVER and other distant site...<br/>
    MeSH
  • Ileus
    Ileus
    A condition caused by the lack of intestinal PERISTALSIS or INTESTINAL MOTILITY without any mechanical obstruction. This interference of the flow of INTESTINAL CONTENTS often ...<br/>Year introduced: 2004
    MeSH
  • Dysentery, Bacillary
    Dysentery, Bacillary
    DYSENTERY caused by gram-negative rod-shaped enteric bacteria (ENTEROBACTERIACEAE), most often by the genus SHIGELLA. Shigella dysentery, Shigellosis, is classified into subgr...<br/>
    MeSH
  • Dientamoebiasis
    Dientamoebiasis
    Gastrointestinal infection with organisms of the genus DIENTAMOEBA.<br/>Year introduced: 1991(1975)
    MeSH

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003502008Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 20, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003502008.2

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

Description

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 258 of the TAP2 protein (p.Thr258Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TAP2-related conditions. 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: "Not Available"; Align-GVGD: "Class C0"). 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.

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

Last Updated: Sep 29, 2024