GeneBe

TGFBRAP1

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

Basic information

Region (hg38): 2:105264391-105329735

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.

  • not_specified (92 variants)
  • not_provided (7 variants)
  • Long_QT_syndrome (1 variants)

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. These statistics are base on transcript: NM_000004257.6. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
4
clinvar
 6
missense
87
clinvar
6
clinvar
1
clinvar
 94
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 87 8 5
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TGFBRAP1protein_codingprotein_codingENST00000393359 1165621
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1650.8351257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.364265130.8310.00003145613
Missense in Polyphen99154.10.642431768
Synonymous0.2732222270.9770.00001561726
Loss of Function4.26936.90.2440.00000175421

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0001060.000105
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.650

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tgfbrap1
Phenotype

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