TBC1D10A

TBC1 domain family member 10A

Basic information

Region (hg38): 22:30291990-30326947

Previous symbols: [ "TBC1D10" ]

Links

ENSG00000099992 ∙ NCBI:83874 ∙ OMIM:610020 ∙ HGNC:23609 ∙ Uniprot:Q9BXI6 ∙ 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 TBC1D10A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D10A 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			32	2	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	1

Variants in TBC1D10A

This is a list of pathogenic ClinVar variants found in the TBC1D10A region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30292396-C-G		not specified	Uncertain significance (Dec 09, 2023)
22-30292406-G-A		not specified	Uncertain significance (Jun 28, 2022)
22-30292506-G-T		not specified	Uncertain significance (Sep 29, 2022)
22-30292560-G-A		not specified	Uncertain significance (Jun 13, 2024)
22-30292566-C-T		not specified	Uncertain significance (Feb 16, 2023)
22-30292614-G-C		not specified	Uncertain significance (May 21, 2024)
22-30292634-G-A		not specified	Uncertain significance (Oct 04, 2022)
22-30292655-G-T		not specified	Uncertain significance (Mar 25, 2024)
22-30292670-C-T			Benign (Apr 19, 2019)
22-30292751-G-A		not specified	Uncertain significance (Apr 07, 2023)
22-30292758-G-A		not specified	Likely benign (Jan 08, 2024)
22-30292773-C-T		not specified	Uncertain significance (Jan 02, 2024)
22-30292790-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-30292794-G-A		not specified	Uncertain significance (Nov 03, 2023)
22-30292826-C-T		not specified	Uncertain significance (Feb 23, 2023)
22-30293653-C-T		not specified	Uncertain significance (Jan 10, 2023)
22-30293697-C-T		not specified	Uncertain significance (Apr 23, 2024)
22-30293706-T-A		not specified	Uncertain significance (Dec 05, 2022)
22-30293708-G-C		not specified	Uncertain significance (Dec 22, 2023)
22-30293710-T-C		not specified	Uncertain significance (Jun 06, 2023)
22-30293716-C-T		not specified	Uncertain significance (Aug 09, 2021)
22-30293751-G-A		not specified	Uncertain significance (Sep 22, 2022)
22-30293767-T-G		not specified	Uncertain significance (Mar 21, 2022)
22-30293770-G-C		not specified	Uncertain significance (Dec 05, 2022)
22-30294004-A-G		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D10A	protein_coding	protein_coding	ENST00000403477	9	35057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00429	0.995	125719	0	24	125743	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	256	319	0.803	0.0000201	3317
Missense in Polyphen		55	91.969	0.59803		896
Synonymous	0.168	129	131	0.981	0.00000799	1040
Loss of Function	3.17	9	26.7	0.337	0.00000132	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000326	0.000323
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as GTPase-activating protein for RAB27A, but not for RAB2A, RAB3A, nor RAB4A. {ECO:0000269|PubMed:16923811}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.481
• hipred: N
• hipred_score: 0.481
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d10a
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: intracellular protein transport;retrograde transport, endosome to Golgi;positive regulation of proteolysis;activation of GTPase activity;activation of cysteine-type endopeptidase activity;regulation of cilium assembly
• Cellular component: cytosol;plasma membrane;microvillus;extracellular exosome
• Molecular function: guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding;Rab GTPase binding;PDZ domain binding;cadherin binding