TAPBPL

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

Basic information

Region (hg38): 12:6451689-6466517

Links

ENSG00000139192 ∙ NCBI:55080 ∙ OMIM:607081 ∙ HGNC:30683 ∙ Uniprot:Q9BX59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAPBPL gene.

• Inborn genetic diseases (16 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAPBPL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in TAPBPL

This is a list of pathogenic ClinVar variants found in the TAPBPL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-6453067-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-6453081-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-6453284-C-G		not specified	Uncertain significance (Oct 27, 2022)
12-6453286-T-C		not specified	Uncertain significance (May 31, 2023)
12-6453473-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-6453527-C-T		not specified	Uncertain significance (Mar 27, 2023)
12-6453645-C-T		not specified	Uncertain significance (May 17, 2023)
12-6453677-A-C		Marfanoid habitus and intellectual disability	Uncertain significance (-)
12-6453708-G-A		not specified	Likely benign (Dec 16, 2023)
12-6453713-G-A		not specified	Uncertain significance (Jun 29, 2022)
12-6457472-A-T		not specified	Uncertain significance (Oct 04, 2022)
12-6457489-G-A		not specified	Uncertain significance (Oct 20, 2021)
12-6457523-G-A		not specified	Uncertain significance (Mar 27, 2023)
12-6457588-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-6457589-G-A		not specified	Uncertain significance (Apr 13, 2023)
12-6458681-C-T		not specified	Uncertain significance (Jun 07, 2023)
12-6458936-T-C		not specified	Uncertain significance (Dec 16, 2021)
12-6460857-C-T		not specified	Uncertain significance (Nov 22, 2022)
12-6462085-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-6462127-C-T		not specified	Uncertain significance (Oct 06, 2021)
12-6462840-G-A			Benign/Likely benign (Jan 01, 2024)
12-6462882-A-G		Myasthenic syndrome, congenital, 25, presynaptic • Spastic ataxia 1	Benign (Dec 05, 2021)
12-6463025-T-C			Benign (May 15, 2021)
12-6464474-G-A		Spastic paraplegia	Uncertain significance (Aug 22, 2022)
12-6464476-A-G		Spastic paraplegia	Likely benign (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAPBPL	protein_coding	protein_coding	ENST00000266556	7	14828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-10	0.254	125623	0	124	125747	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	231	267	0.866	0.0000144	2975
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000845	0.000841
Ashkenazi Jewish	0.000417	0.000397
East Asian	0.000218	0.000217
Finnish	0.00125	0.00125
European (Non-Finnish)	0.000254	0.000237
Middle Eastern	0.000218	0.000217
South Asian	0.00115	0.00111
Other	0.000499	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0481
• hipred: N
• hipred_score: 0.123
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.368

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tapbpl

Gene ontology

• Biological process: immune system process;negative regulation of antigen processing and presentation of peptide antigen via MHC class I
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;plasma membrane;integral component of membrane
• Molecular function: protein binding;protein-containing complex binding