TBC1D9B

protein-coding

TBC1 domain family member 9B, the group of GRAM domain containing|EF-hand domain containing

Gene summary

Predicted to enable GTPase activator activity. Predicted to be involved in system process. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015043.4

Inheritance

—

ClinVar variants

U:41B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr5:179,862,066-179,907,897

External References & Databases

Ensembl (ENSG00000197226)

Transcript & Mutation Effects

hg38 • Region Span ~45.8 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 TBC1D9B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 16

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015043.4. 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			5 clinvar	5 clinvar		10
missense			27 clinvar	2 clinvar	1 clinvar	30
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	41	7	1	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015043.4	RefSeq	NP_055858.2	21	MANE Select
ENST00000355235.8	Ensembl	ENSP00000347375.3	21	MANE Select
NM_198868.3	RefSeq	NP_942568.2	22	Standard
ENST00000356834.7	Ensembl	ENSP00000349291.3	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
activation of GTPase activity
regulation of cilium assembly

Molecular Function

GTPase activator activity
calcium ion binding
protein binding
Rab GTPase binding

Cellular Component

cell
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356834
Coding exons: 22
Length: 45794
Individuals with no LoFs: 125679
Homozygous LoFs: 0
Heterozygous LoFs: 69
Defined: 125748
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.645	694	743	0.933	0.0000469	8170
Missense (PolyPhen)		211	260.32	0.81055		2847
Synonymous	-0.393	334	325	1.03	0.0000230	2463
Loss of Function	3.70	29	59.9	0.484	0.00000323	654

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00049	0.00049	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00033	0.00030	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.728
RVIS EVS: -0.45
RVIS percentile EVS: 24.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.258

Gene Damage Prediction

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