TBC1D3

TBC1 domain family member 3

Basic information

Region (hg38): 17:38181659-38192555

Links

ENSG00000274611

∙ NCBI:729873 ∙ OMIM:607741 ∙ HGNC:19031 ∙ Uniprot:Q8IZP1 ∙ 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 TBC1D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D3 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				1 clinvar		1
missense			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in TBC1D3

This is a list of pathogenic ClinVar variants found in the TBC1D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-38184096-G-A			Likely benign (Sep 01, 2022)	2647697
17-38187891-C-T		not specified	Uncertain significance (Aug 13, 2021)	2244794

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11. {ECO:0000269|PubMed:12359748}.;
Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.187
ghis

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0279

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

Biological process: intracellular protein transport;activation of GTPase activity;regulation of cilium assembly
Cellular component: plasma membrane;early endosome membrane
Molecular function: GTPase activator activity;Rab GTPase binding