TBC1D10C

TBC1 domain family member 10C

Basic information

Region (hg38): 11:67403915-67410089

Links

ENSG00000175463 ∙ NCBI:374403 ∙ OMIM:610831 ∙ HGNC:24702 ∙ Uniprot:Q8IV04 ∙ 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 TBC1D10C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D10C 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				2		2
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	0

Variants in TBC1D10C

This is a list of pathogenic ClinVar variants found in the TBC1D10C region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67404218-G-A		not specified	Uncertain significance (Apr 23, 2024)
11-67404237-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-67404275-G-A		not specified	Uncertain significance (Aug 30, 2022)
11-67404275-G-T		not specified	Uncertain significance (Jul 08, 2021)
11-67404306-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-67404313-C-T		not specified	Likely benign (May 16, 2024)
11-67405100-T-C			Likely benign (Jan 01, 2023)
11-67405119-C-T		not specified	Uncertain significance (Jul 29, 2023)
11-67405147-C-T		not specified	Likely benign (Nov 01, 2022)
11-67405170-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-67405171-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-67405173-C-T		not specified	Uncertain significance (May 09, 2023)
11-67405414-C-T		not specified	Uncertain significance (Apr 10, 2023)
11-67405427-C-T		not specified	Uncertain significance (Jun 16, 2023)
11-67405700-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-67406828-A-T		not specified	Uncertain significance (Feb 27, 2024)
11-67406851-G-T		not specified	Uncertain significance (May 15, 2024)
11-67406869-C-T		not specified	Uncertain significance (Mar 28, 2024)
11-67406886-C-T			Likely benign (Jan 01, 2023)
11-67406895-G-T		not specified	Uncertain significance (Oct 27, 2023)
11-67406903-A-G		not specified	Uncertain significance (Jun 07, 2023)
11-67406914-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-67406963-G-A		not specified	Uncertain significance (Jun 27, 2022)
11-67408996-C-T		not specified	Uncertain significance (Oct 25, 2023)
11-67408997-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D10C	protein_coding	protein_coding	ENST00000312390	9	6175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.154	0.846	125506	0	41	125547	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.920	237	280	0.845	0.0000191	2753
Missense in Polyphen		96	129.22	0.74294		1239
Synonymous	-0.212	126	123	1.02	0.00000792	978
Loss of Function	3.34	6	23.4	0.256	0.00000133	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000575	0.000555
European (Non-Finnish)	0.000230	0.000220
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000344	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the Ras signaling pathway through its intrinsic Ras GTPase-activating protein (GAP) activity. Acts as a negative feedback inhibitor of the calcineurin signaling pathway that also mediates crosstalk between calcineurin and Ras. {ECO:0000269|PubMed:17230191}.
• Pathway: Neutrophil degranulation;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Innate Immune System;Immune System;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.598
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.285
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d10c
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: intracellular protein transport;retrograde transport, endosome to Golgi;neutrophil degranulation;negative regulation of B cell activation;negative regulation of ERK1 and ERK2 cascade;negative regulation of calcineurin-NFAT signaling cascade;activation of GTPase activity;regulation of cilium assembly
• Cellular component: cytosol;plasma membrane;membrane;filopodium membrane;ficolin-1-rich granule membrane
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding