ATP6V1C2

ATPase H+ transporting V1 subunit C2, the group of V-type ATPase subunits

Basic information

Region (hg38): 2:10721100-10785110

Links

ENSG00000143882NCBI:245973OMIM:618070HGNC:18264Uniprot:Q8NEY4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP6V1C2 gene.

  • not_specified (53 variants)
  • not_provided (5 variants)
  • Distal_renal_tubular_acidosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6V1C2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039362.2. 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
1
clinvar
1
missense
1
clinvar
53
clinvar
1
clinvar
55
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 53 1 1

Highest pathogenic variant AF is 0.000483856

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATP6V1C2protein_codingprotein_codingENST00000272238 1363462
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.85e-80.9171256820661257480.000262
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8272052410.8500.00001312793
Missense in Polyphen5069.480.71963832
Synonymous0.1679799.10.9790.00000616816
Loss of Function1.801625.90.6180.00000140296

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008820.000882
Ashkenazi Jewish0.000.00
East Asian0.0001650.000163
Finnish0.0004620.000462
European (Non-Finnish)0.0001760.000176
Middle Eastern0.0001650.000163
South Asian0.0001650.000163
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.;
Pathway
mTOR signaling pathway - Homo sapiens (human);Synaptic vesicle cycle - Homo sapiens (human);Phagosome - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Collecting duct acid secretion - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Signal Transduction;Transferrin endocytosis and recycling;Ion channel transport;Insulin receptor recycling;Signaling by Insulin receptor;ROS, RNS production in phagocytes;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.921
rvis_EVS
-0.02
rvis_percentile_EVS
52.09

Haploinsufficiency Scores

pHI
0.134
hipred
N
hipred_score
0.341
ghis
0.516

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.289

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Atp6v1c2
Phenotype

Gene ontology

Biological process
insulin receptor signaling pathway;ATP hydrolysis coupled proton transport;regulation of macroautophagy;positive regulation of Wnt signaling pathway;transferrin transport;ion transmembrane transport
Cellular component
vacuolar proton-transporting V-type ATPase, V1 domain;lysosomal membrane;cytosol;extracellular exosome
Molecular function
proton-exporting ATPase activity, phosphorylative mechanism;proton-transporting ATPase activity, rotational mechanism;protein dimerization activity