TGFBRAP1

transforming growth factor beta receptor associated protein 1, the group of CORVET complex

Basic information

Region (hg38): 2:105264390-105329735

Links

ENSG00000135966 ∙ NCBI:9392 ∙ OMIM:606237 ∙ HGNC:16836 ∙ Uniprot:Q8WUH2 ∙ 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 TGFBRAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGFBRAP1 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				2	4	6
missense			36	1	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	5

Variants in TGFBRAP1

This is a list of pathogenic ClinVar variants found in the TGFBRAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-105267391-G-A		not specified	Uncertain significance (Nov 10, 2022)
2-105267421-T-C		not specified	Uncertain significance (Nov 22, 2023)
2-105267547-C-G		not specified	Uncertain significance (Jul 14, 2021)
2-105267557-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-105267559-T-C		not specified	Uncertain significance (Dec 23, 2023)
2-105269350-G-C		not specified	Uncertain significance (Feb 03, 2022)
2-105269464-C-T			Benign (Jul 13, 2018)
2-105269484-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-105269591-G-T		not specified	Uncertain significance (Jan 16, 2024)
2-105269692-T-G			Likely benign (Dec 01, 2022)
2-105272899-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-105272903-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-105272911-G-C		not specified	Uncertain significance (Mar 02, 2023)
2-105272917-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-105272937-C-T			Benign (Jul 13, 2018)
2-105272953-G-A		not specified	Uncertain significance (Sep 30, 2021)
2-105273553-C-G		not specified	Uncertain significance (Dec 14, 2022)
2-105273588-G-A		not specified	Uncertain significance (Nov 22, 2023)
2-105273600-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-105273605-T-C		not specified	Uncertain significance (Feb 10, 2022)
2-105273624-C-T		not specified	Uncertain significance (Oct 27, 2022)
2-105273678-C-T		not specified	Uncertain significance (Oct 27, 2021)
2-105275611-G-A			Likely benign (Dec 01, 2022)
2-105280415-G-A		not specified	Uncertain significance (Aug 28, 2021)
2-105280461-C-T		not specified	Uncertain significance (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGFBRAP1	protein_coding	protein_coding	ENST00000393359	11	65621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.165	0.835	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	426	513	0.831	0.0000314	5613
Missense in Polyphen		99	154.1	0.64243		1768
Synonymous	0.273	222	227	0.977	0.0000156	1726
Loss of Function	4.26	9	36.9	0.244	0.00000175	421

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling. May recruit SMAD4 to the vicinity of the receptor complex and facilitate its interaction with receptor-regulated Smads, such as SMAD2. {ECO:0000269|PubMed:11278302, ECO:0000269|PubMed:9545258}.
• Pathway: Regulation of cytoplasmic and nuclear SMAD2/3 signaling;TGF-beta receptor signaling (Consensus)

Recessive Scores

• pRec: 0.235

Intolerance Scores

• loftool: 0.349
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.83

Haploinsufficiency Scores

• pHI: 0.0745
• hipred: Y
• hipred_score: 0.694
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.650

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgfbrap1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;intracellular protein transport;signal transduction;transforming growth factor beta receptor signaling pathway;endosome to lysosome transport;endosomal vesicle fusion
• Cellular component: early endosome;membrane;CORVET complex;intracellular membrane-bounded organelle
• Molecular function: transforming growth factor beta receptor binding;protein binding;SMAD binding