TBC1D15

TBC1 domain family member 15

Basic information

Region (hg38): 12:71839707-71927248

Links

ENSG00000121749 ∙ NCBI:64786 ∙ OMIM:612662 ∙ HGNC:25694 ∙ Uniprot:Q8TC07 ∙ 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 TBC1D15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D15 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						0
missense			23	1		24
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in TBC1D15

This is a list of pathogenic ClinVar variants found in the TBC1D15 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-71839785-G-T		not specified	Uncertain significance (Nov 12, 2021)
12-71872109-T-A		not specified	Uncertain significance (Feb 05, 2024)
12-71872133-G-A		not specified	Likely benign (Mar 20, 2024)
12-71880542-G-A		not specified	Uncertain significance (Nov 30, 2021)
12-71880562-A-G		not specified	Uncertain significance (Aug 12, 2022)
12-71880587-G-A		not specified	Likely benign (Oct 27, 2022)
12-71880602-A-G		not specified	Uncertain significance (Jan 12, 2024)
12-71884902-G-A		not specified	Uncertain significance (Mar 20, 2024)
12-71884964-A-G		not specified	Uncertain significance (Apr 15, 2024)
12-71894374-A-C		not specified	Uncertain significance (Jul 05, 2023)
12-71894795-C-G		not specified	Uncertain significance (Sep 15, 2021)
12-71895957-G-T		not specified	Uncertain significance (Jun 22, 2024)
12-71896034-A-T		not specified	Uncertain significance (Oct 03, 2022)
12-71896050-A-T		not specified	Uncertain significance (May 24, 2024)
12-71897863-A-G		not specified	Uncertain significance (Apr 28, 2022)
12-71897887-A-G		not specified	Uncertain significance (Feb 28, 2024)
12-71897912-C-T		not specified	Uncertain significance (Jun 04, 2024)
12-71897916-G-T		not specified	Uncertain significance (Aug 16, 2022)
12-71907072-G-A		not specified	Uncertain significance (Oct 20, 2021)
12-71907122-G-A		not specified	Uncertain significance (Jul 29, 2022)
12-71913900-T-C		not specified	Uncertain significance (Feb 22, 2023)
12-71917758-T-G		not specified	Uncertain significance (Sep 23, 2023)
12-71918500-C-G		not specified	Uncertain significance (Jul 20, 2021)
12-71918506-C-A		not specified	Uncertain significance (Apr 12, 2022)
12-71920734-A-T		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D15	protein_coding	protein_coding	ENST00000550746	18	87143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0615	0.938	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.917	304	352	0.863	0.0000169	4583
Missense in Polyphen		106	147.67	0.71782		2055
Synonymous	-1.89	148	122	1.22	0.00000631	1202
Loss of Function	4.50	11	42.8	0.257	0.00000213	533

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000151	0.000151
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000182	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000182	0.000163
South Asian	0.0000980	0.0000980
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase activating protein for RAB7A. Does not act on RAB4, RAB5 or RAB6 (By similarity). {ECO:0000250}.
• Pathway: Mitophagy - animal - Homo sapiens (human);Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.710
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.43

Haploinsufficiency Scores

• pHI: 0.247
• hipred: N
• hipred_score: 0.426
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d15

Gene ontology

• Biological process: intracellular protein transport;regulation of GTPase activity;activation of GTPase activity;regulation of cilium assembly
• Cellular component: extracellular region;cytoplasm
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding