TAPBPL

protein-coding

TAP binding protein like, the group of C1-set domain containing

Gene summary

Tapasin, or TAPBP (MIM 601962), is a member of the variable-constant Ig superfamily that links major histocompatibility complex (MHC) class I molecules to the transporter associated with antigen processing (TAP; see MIM 170260) in the endoplasmic reticulum (ER). The TAPBP gene is located near the MHC complex on chromosome 6p21.3. TAPBPL is a member of the Ig superfamily that is localized on chromosome 12p13.3, a region somewhat paralogous to the MHC.[supplied by OMIM, Mar 2008]

MANE transcript

NM_018009.5

Inheritance

—

ClinVar variants

U:63B:3

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr12:6,451,690-6,466,517

External References & Databases

Ensembl (ENSG00000139192)

Transcript & Mutation Effects

hg38 • Region Span ~14.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TAPBPL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

Marfanoid habitus and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018009.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			61 clinvar	3 clinvar		64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	3	0	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018009.5	RefSeq	NP_060479.3	7	MANE Select
ENST00000266556.8	Ensembl	ENSP00000266556.7	7	MANE Select
NM_001351355.2	RefSeq	NP_001338284.1	5	Standard
ENST00000544021.5	Ensembl	ENSP00000445341.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

immune system process
negative regulation of antigen processing and presentation of peptide antigen via MHC class I

Molecular Function

protein binding
protein-containing complex binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266556
Coding exons: 7
Length: 14828
Individuals with no LoFs: 125623
Homozygous LoFs: 0
Heterozygous LoFs: 124
Defined: 125747
p: 0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.779	231	267	0.866	0.0000144	2975
Missense (PolyPhen)		47	60.872	0.77212		725
Synonymous	0.102	113	114	0.988	0.00000665	1013
Loss of Function	0.779	17	20.8	0.816	0.00000132	186

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00066	0.00064	rare
Ashkenazi Jewish	0.00042	0.00040	rare
East Asian	0.00022	0.00022	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.0011	0.0011	notable
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the antigen processing and presentation pathway, which binds to MHC class I coupled with beta2- microglobulin/B2M. Association between TAPBPR and MHC class I occurs in the absence of a functional peptide-loading complex (PLC). Expression seems to slow down and down-regulate MHC class I surface expression. {ECO:0000269|PubMed:23401559}.;

Recessive Scores

pRec: 0.0840

Intolerance Scores

LoFtool: 0.883
RVIS EVS: 0.98
RVIS percentile EVS: 90.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.368

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium