TBC1D12

protein-coding

TBC1 domain family member 12

Gene summary

Predicted to enable GTPase activator activity. Predicted to be involved in regulation of autophagosome assembly. Predicted to be located in endosome and vacuole. Predicted to be active in autophagosome and recycling endosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015188.2

Inheritance

—

ClinVar variants

U:126B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr10:94,402,541-94,536,332

External References & Databases

Ensembl (ENSG00000108239)

Transcript & Mutation Effects

hg38 • Region Span ~133.8 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 TBC1D12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015188.2. 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			120 clinvar	5 clinvar		125
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	126	5	0	131

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015188.2	RefSeq	NP_056003.1	13	MANE Select
ENST00000225235.5	Ensembl	ENSP00000225235.4	13	MANE Select
ENST00000904398.1	Ensembl	ENSP00000574457.1	10	Standard
ENST00000904398.2	Ensembl	ENSP00000574457.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
activation of GTPase activity

Molecular Function

GTPase activator activity
Rab GTPase binding

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000225235
Coding exons: 13
Length: 133427
Individuals with no LoFs: 124767
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124791
p: 0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	305	369	0.827	0.0000188	4936
Missense (PolyPhen)		92	155.6	0.59126		2055
Synonymous	0.446	135	142	0.952	0.00000708	1528
Loss of Function	3.49	15	38.4	0.391	0.00000246	420

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00027	0.00026	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.287

Gene Damage Prediction

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