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.

not_specified (92 variants)

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. These statistics are base on transcript: NM_000031937.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			85 clinvar	4 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	4	0

Loading clinvar variants...

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