TBC1D9

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

Basic information

Region (hg38): 4:140620782-140756385

Links

ENSG00000109436 ∙ NCBI:23158 ∙ OMIM:618035 ∙ HGNC:21710 ∙ Uniprot:Q6ZT07 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	46	2	1

Variants in TBC1D9

This is a list of pathogenic ClinVar variants found in the TBC1D9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-140622211-G-A		not specified	Uncertain significance (Jan 26, 2022)
4-140622326-G-C		not specified	Uncertain significance (Dec 01, 2022)
4-140622356-C-T		not specified	Uncertain significance (Jun 22, 2023)
4-140622376-C-T		not specified	Uncertain significance (Aug 15, 2023)
4-140622377-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-140622409-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-140622461-G-A		Attention deficit hyperactivity disorder	Uncertain significance (Jan 03, 2017)
4-140622517-C-A		not specified	Uncertain significance (Sep 08, 2023)
4-140622640-G-A		not specified	Uncertain significance (Feb 27, 2023)
4-140622670-G-A		not specified	Uncertain significance (Feb 28, 2024)
4-140622699-T-G		not specified	Uncertain significance (Mar 02, 2023)
4-140622707-G-A		not specified	Uncertain significance (May 24, 2024)
4-140622716-C-T		not specified	Likely benign (Dec 20, 2023)
4-140624222-A-G			Benign (Apr 19, 2018)
4-140627524-G-A		not specified	Uncertain significance (Dec 13, 2022)
4-140628309-C-T		not specified	Uncertain significance (Mar 21, 2022)
4-140633974-T-G		not specified	Uncertain significance (Jan 05, 2022)
4-140634029-C-T		not specified	Uncertain significance (Aug 13, 2021)
4-140634068-C-A		not specified	Uncertain significance (Jul 19, 2023)
4-140634113-G-C		not specified	Uncertain significance (Nov 06, 2023)
4-140634146-C-G		not specified	Uncertain significance (Feb 17, 2023)
4-140634187-G-T		not specified	Uncertain significance (Feb 22, 2023)
4-140639343-G-A		not specified	Uncertain significance (Nov 10, 2022)
4-140639358-G-T		not specified	Uncertain significance (Jul 15, 2021)
4-140639412-C-A		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D9	protein_coding	protein_coding	ENST00000442267	21	135356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000280	1.00	124662	0	29	124691	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.16	483	722	0.669	0.0000416	8332
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.0000556	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000198	0.000195
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000657	0.0000654
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.639
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d9

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cell
• Molecular function: GTPase activator activity;calcium ion binding;protein binding;Rab GTPase binding