TBC1D9

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			1 clinvar	2 clinvar	1 clinvar	4
missense			128 clinvar	1 clinvar		129
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	137	3	1	141

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015130.3	RefSeq	NP_055945.2	21	MANE Select
ENST00000442267.3	Ensembl	ENSP00000411197.2	21	MANE Select
ENST00000855917.1	Ensembl	ENSP00000525976.1	21	Standard
ENST00000855917.2	Ensembl	ENSP00000525976.1	21	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
calcium ion binding
protein binding
Rab GTPase binding

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000442267
Coding exons: 21
Length: 135356
Individuals with no LoFs: 124662
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 124691
p: 0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.16	483	722	0.669	0.0000416	8332
Missense (PolyPhen)		217	374.13	0.58001		4411
Synonymous	0.978	268	289	0.927	0.0000175	2404
Loss of Function	4.69	19	57.3	0.332	0.00000291	687

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000066	0.000065	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).;

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.266
RVIS EVS: -0.93
RVIS percentile EVS: 9.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.544

Gene Damage Prediction

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