GeneBe

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.

  • not_specified (76 variants)
  • not_provided (2 variants)

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. These statistics are base on transcript: NM_001369496.1. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
 3
missense
73
clinvar
2
clinvar
 75
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 73 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TBC1D10Cprotein_codingprotein_codingENST00000312390 96175
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1540.8461255060411255470.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9202372800.8450.00001912753
Missense in Polyphen96129.220.742941239
Synonymous-0.2121261231.020.00000792978
Loss of Function3.34623.40.2560.00000133232

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002960.0000296
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0005750.000555
European (Non-Finnish)0.0002300.000220
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0003440.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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