NM_001290043.2(TAP2):c.701T>A (p.Leu234Gln) AND MHC class I deficiency

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

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 31, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000696803.8

Allele description

NM_001290043.2(TAP2):c.701T>A (p.Leu234Gln)

Genes:

LOC107648851:meiotic recombination hotspot TAP2 [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.701T>A (p.Leu234Gln)

HGVS:

NC_000006.12:g.32835681A>T
NG_009793.4:g.8090T>A
NG_046880.1:g.243A>T
NM_000544.3:c.701T>A
NM_001290043.2:c.701T>AMANE SELECT
NM_018833.3:c.701T>A
NP_000535.3:p.Leu234Gln
NP_001276972.1:p.Leu234Gln
NP_061313.2:p.Leu234Gln
LRG_167t1:c.701T>A
LRG_167t2:c.701T>A
LRG_167:g.8090T>A
LRG_167p1:p.Leu234Gln
LRG_167p2:p.Leu234Gln
NC_000006.11:g.32803458A>T
NG_009793.3:g.8090T>A
NM_001290043.1:c.701T>A

Protein change:

L234Q

Links:

dbSNP: rs138708621

NCBI 1000 Genomes Browser:

rs138708621

Molecular consequence:

NM_000544.3:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001290043.2:c.701T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_018833.3:c.701T>A - 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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NACHT, LRR and PYD domains-containing protein 3 isoform X3 [Homo sapiens]
NACHT, LRR and PYD domains-containing protein 3 isoform X3 [Homo sapiens]
gi|2217263548|ref|XP_047299513.1|

Protein
cytochrome c oxidase subunit I, partial (mitochondrion) [Drosophila melanogaster...
cytochrome c oxidase subunit I, partial (mitochondrion) [Drosophila melanogaster]
gi|667699630|gnl|REF_FlyBase|CG3406 ref|YP_009047267.1|

Protein
Rubricatochromis guttatus[orgn] (87)
Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000825382	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 31, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26122175, 28492532
SCV003818947	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 13, 2020)	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

SCV000825382

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 31, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV003818947

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 13, 2020)

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

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.

van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC; WGS500 Consortium., Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY.

Clin Immunol. 2015 Oct;160(2):301-14. doi: 10.1016/j.clim.2015.05.020. Epub 2015 Jun 26.

PubMed [citation]

PMID:: 26122175
PMCID:: PMC4601528

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

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000825382.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces leucine, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 234 of the TAP2 protein (p.Leu234Gln). This variant is present in population databases (rs138708621, gnomAD 0.04%). This missense change has been observed in individual(s) with common variable immunodeficiency (CVID) (PMID: 26122175). ClinVar contains an entry for this variant (Variation ID: 574783). 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"). 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

From Revvity Omics, Revvity, SCV003818947.2

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

#	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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