TBC1D3F

TBC1 domain family member 3F

Basic information

Region (hg38): 17:36428618-36439566

Links

ENSG00000275954 ∙ NCBI:84218 ∙ OMIM:610809 ∙ HGNC:18257 ∙ Uniprot:A6NER0 ∙ 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 TBC1D3F gene.

• not provided (4 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D3F 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			1	3		4
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	3	0

Variants in TBC1D3F

This is a list of pathogenic ClinVar variants found in the TBC1D3F region.

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

Position	Type	Phenotype	Significance	ClinVar
17-36429059-G-A			Likely benign (Sep 01, 2022)
17-36429127-G-T			Likely benign (Apr 01, 2023)
17-36429139-A-G			Likely benign (Apr 01, 2023)
17-36429382-C-T			Likely benign (Feb 01, 2023)
17-36430551-C-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: plasma membrane
• Molecular function: GTPase activator activity;Rab GTPase binding