TBC1D16

protein-coding

TBC1 domain family member 16

Gene summary

Enables GTPase activator activity. Involved in regulation of receptor recycling. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_019020.4

Inheritance

—

ClinVar variants

U:154B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr17:79,932,343-80,035,872

External References & Databases

Ensembl (ENSG00000167291)

Transcript & Mutation Effects

hg38 • Region Span ~103.5 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 TBC1D16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 152

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019020.4. 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	5 clinvar	3 clinvar	10
missense			147 clinvar	4 clinvar		151
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	154	9	3	166

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 91 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019020.4	RefSeq	NP_061893.2	11	MANE Select
ENST00000310924.7	Ensembl	ENSP00000309794.2	11	MANE Select
NM_001271844.2	RefSeq	NP_001258773.1	8	Standard
NM_001271845.2	RefSeq	NP_001258774.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
TBC/RABGAPs
Membrane Trafficking
Rab regulation of trafficking

Biological Process

regulation of receptor recycling
intracellular protein transport
activation of GTPase activity
regulation of cilium assembly

Molecular Function

GTPase activator activity
protein binding
Rab GTPase binding

Cellular Component

early endosome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310924
Coding exons: 11
Length: 103506
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125746
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.559	467	502	0.930	0.0000356	4929
Missense (PolyPhen)		149	195.11	0.76369		1951
Synonymous	0.00361	233	233	1.00	0.0000185	1542
Loss of Function	2.56	16	31.5	0.507	0.00000149	344

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00020	0.00018	rare
European (Non-Finnish)	0.00023	0.00021	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).;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.684
RVIS EVS: -0.46
RVIS percentile EVS: 23.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.233

Gene Damage Prediction

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