TBC1D9B

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

Basic information

Region (hg38): 5:179862066-179907897

Links

ENSG00000197226 ∙ NCBI:23061 ∙ OMIM:618039 ∙ HGNC:29097 ∙ Uniprot:Q66K14 ∙ 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 TBC1D9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D9B 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				5		5
missense			15	2	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	7	1

Variants in TBC1D9B

This is a list of pathogenic ClinVar variants found in the TBC1D9B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179863493-C-A		not specified	Uncertain significance (Jun 18, 2021)
5-179863591-G-C		not specified	Uncertain significance (Jul 28, 2021)
5-179863794-T-C		not specified	Likely benign (Nov 08, 2021)
5-179863948-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-179864062-G-T		not specified	Uncertain significance (Nov 15, 2021)
5-179865302-C-A		not specified	Uncertain significance (Sep 27, 2021)
5-179865331-G-A		not specified	Uncertain significance (Jul 27, 2024)
5-179865348-G-A		not specified	Uncertain significance (Oct 20, 2021)
5-179871526-C-T			Benign (Oct 01, 2022)
5-179875133-T-C		not specified	Uncertain significance (Oct 05, 2021)
5-179875927-C-G		not specified	Uncertain significance (Aug 02, 2021)
5-179875977-G-T		not specified	Uncertain significance (Jul 20, 2021)
5-179876017-C-T			Likely benign (Dec 01, 2022)
5-179879092-C-T		not specified	Uncertain significance (Aug 10, 2021)
5-179879111-C-T			Likely benign (Oct 01, 2022)
5-179879119-C-T		not specified	Uncertain significance (Aug 30, 2021)
5-179879130-A-G		not specified	Uncertain significance (Oct 13, 2021)
5-179879147-G-A			Likely benign (Aug 01, 2022)
5-179891474-G-A			Likely benign (Mar 01, 2022)
5-179893359-G-C			Likely benign (Oct 01, 2022)
5-179893434-C-T		not specified	Uncertain significance (Jul 09, 2021)
5-179893447-C-T		not specified	Uncertain significance (Aug 23, 2021)
5-179894540-C-T			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D9B	protein_coding	protein_coding	ENST00000356834	22	45794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-12	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.645	694	743	0.933	0.0000469	8170
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000804	0.000801
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000329	0.000299
Middle Eastern	0.000218	0.000217
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.492
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d9b

Gene ontology

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