TBC1D13

TBC1 domain family member 13

Basic information

Region (hg38): 9:128787252-128810430

Links

ENSG00000107021 ∙ NCBI:54662 ∙ OMIM:616218 ∙ HGNC:25571 ∙ Uniprot:Q9NVG8 ∙ 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 TBC1D13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D13 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TBC1D13

This is a list of pathogenic ClinVar variants found in the TBC1D13 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128788351-A-G		not specified	Uncertain significance (May 11, 2022)
9-128797088-G-C		not specified	Uncertain significance (May 14, 2024)
9-128797191-C-T		not specified	Uncertain significance (Apr 25, 2022)
9-128797198-G-A		not specified	Uncertain significance (Dec 16, 2023)
9-128797204-G-A		not specified	Uncertain significance (Dec 14, 2022)
9-128803344-G-A		not specified	Uncertain significance (Mar 01, 2023)
9-128803361-G-A		not specified	Uncertain significance (May 09, 2022)
9-128803401-A-G		not specified	Uncertain significance (May 15, 2023)
9-128803439-G-A		not specified	Uncertain significance (Feb 28, 2023)
9-128803439-G-T		not specified	Uncertain significance (Dec 08, 2023)
9-128803446-A-G		not specified	Uncertain significance (Aug 22, 2023)
9-128805895-C-G		not specified	Uncertain significance (Sep 21, 2023)
9-128805946-C-T		not specified	Uncertain significance (Mar 14, 2023)
9-128807850-A-C		not specified	Uncertain significance (Dec 18, 2023)
9-128807865-C-G		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D13	protein_coding	protein_coding	ENST00000372648	12	23229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000659	0.995	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	155	232	0.669	0.0000137	2649
Missense in Polyphen		58	87.252	0.66474		941
Synonymous	0.535	89	95.7	0.930	0.00000568	743
Loss of Function	2.52	9	21.7	0.415	9.21e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase-activating protein for RAB35. Together with RAB35 may be involved in regulation of insulin-induced glucose transporter SLC2A4/GLUT4 translocation to the plasma membrane in adipocytes. {ECO:0000250|UniProtKB:Q8R3D1}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.312
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.239
• hipred: Y
• hipred_score: 0.673
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d13

Gene ontology

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