NM_001290043.2(TAP2):c.1060C>T (p.Arg354Cys) AND MHC class I deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 19, 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:: RCV003076259.2

Allele description

NM_001290043.2(TAP2):c.1060C>T (p.Arg354Cys)

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.1060C>T (p.Arg354Cys)

HGVS:

NC_000006.12:g.32832710G>A
NG_009793.4:g.11061C>T
NM_000544.3:c.1060C>T
NM_001290043.2:c.1060C>TMANE SELECT
NM_018833.3:c.1060C>T
NP_000535.3:p.Arg354Cys
NP_001276972.1:p.Arg354Cys
NP_061313.2:p.Arg354Cys
LRG_167t1:c.1060C>T
LRG_167t2:c.1060C>T
LRG_167:g.11061C>T
LRG_167p1:p.Arg354Cys
LRG_167p2:p.Arg354Cys
NC_000006.11:g.32800487G>A

Protein change:

R354C

Molecular consequence:

NM_000544.3:c.1060C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001290043.2:c.1060C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_018833.3:c.1060C>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003449685	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 19, 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

SCV003449685

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 19, 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 Invitae, SCV003449685.2

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

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 354 of the TAP2 protein (p.Arg354Cys). 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. 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: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with TAP2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%).

#	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: Jun 9, 2024

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