ATP6V1C2

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

Basic information

Region (hg38): 2:10721100-10785110

Links

ENSG00000143882 ∙ NCBI:245973 ∙ OMIM:618070 ∙ HGNC:18264 ∙ Uniprot:Q8NEY4 ∙ 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 ATP6V1C2 gene.

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.

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					1	1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			4			4
Total	0	0	24	0	1

Variants in ATP6V1C2

This is a list of pathogenic ClinVar variants found in the ATP6V1C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10722893-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-10722939-C-A		not specified	Uncertain significance (Dec 17, 2023)
2-10722952-A-G		not specified	Uncertain significance (Feb 23, 2023)
2-10722955-A-C		not specified	Uncertain significance (Jun 21, 2022)
2-10726528-C-T			Benign (Feb 20, 2018)
2-10764368-C-G		not specified	Uncertain significance (Jun 02, 2023)
2-10768726-C-T		not specified	Conflicting classifications of pathogenicity (Sep 01, 2022)
2-10768735-A-G		not specified	Uncertain significance (May 11, 2022)
2-10771871-T-C		Distal renal tubular acidosis	Likely pathogenic (Oct 22, 2019)
2-10771891-G-A		not specified	Uncertain significance (May 01, 2024)
2-10771930-G-A		not specified	Uncertain significance (May 04, 2023)
2-10772538-G-A			Benign (Apr 16, 2018)
2-10772575-A-C		not specified	Uncertain significance (Aug 17, 2022)
2-10775019-A-T		not specified	Uncertain significance (Jun 10, 2022)
2-10775038-G-A		not specified	Uncertain significance (Jan 10, 2022)
2-10777606-A-G			Uncertain significance (-)
2-10777637-A-G		not specified	Uncertain significance (Dec 22, 2023)
2-10777652-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-10777703-A-T		not specified	Uncertain significance (Jan 16, 2024)
2-10777707-T-A		not specified	Uncertain significance (May 07, 2024)
2-10778579-T-G		not specified	Uncertain significance (Sep 01, 2021)
2-10778662-G-A		not specified	Uncertain significance (Apr 15, 2022)
2-10778665-C-T		not specified	Uncertain significance (Jul 16, 2021)
2-10778673-C-T			Likely benign (Feb 01, 2023)
2-10782262-T-C		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6V1C2	protein_coding	protein_coding	ENST00000272238	13	63462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.85e-8	0.917	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.827	205	241	0.850	0.0000131	2793
Missense in Polyphen		50	69.48	0.71963		832
Synonymous	0.167	97	99.1	0.979	0.00000616	816
Loss of Function	1.80	16	25.9	0.618	0.00000140	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000882	0.000882
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000165	0.000163
South Asian	0.000165	0.000163
Other	0.000326	0.000326

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

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

Mouse Genome Informatics

• Gene name: Atp6v1c2

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