TBC1D10A

protein-coding

TBC1 domain family member 10A

Gene summary

Enables GTPase activator activity and PDZ domain binding activity. Involved in positive regulation of proteolysis and retrograde transport, endosome to Golgi. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

TBC1D10

MANE transcript

NM_031937.3

Inheritance

—

ClinVar variants

U:104B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr22:30,291,990-30,326,947

External References & Databases

Ensembl (ENSG00000099992)

Transcript & Mutation Effects

hg38 • Region Span ~35.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBC1D10A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031937.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			97 clinvar	4 clinvar		101
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	104	4	0	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031937.3	RefSeq	NP_114143.1	9	MANE Select
ENST00000215790.12	Ensembl	ENSP00000215790.8	9	MANE Select
NM_001204240.2	RefSeq	NP_001191169.1	9	Standard
ENST00000393906.2	Ensembl	ENSP00000377484.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Vesicle-mediated transport
TBC/RABGAPs
Membrane Trafficking
Rab regulation of trafficking

Biological Process

intracellular protein transport
retrograde transport, endosome to Golgi
positive regulation of proteolysis
activation of GTPase activity
activation of cysteine-type endopeptidase activity

Molecular Function

guanyl-nucleotide exchange factor activity
GTPase activator activity
protein binding
Rab GTPase binding
PDZ domain binding

Cellular Component

cytosol
plasma membrane
microvillus
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403477
Coding exons: 9
Length: 35057
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125743
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.25	256	319	0.803	0.0000201	3317
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as GTPase-activating protein for RAB27A, but not for RAB2A, RAB3A, nor RAB4A. {ECO:0000269|PubMed:16923811}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.336
RVIS EVS: -0.4
RVIS percentile EVS: 26.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.797

Gene Damage Prediction

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