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ATP6V1C2 ATPase H+ transporting V1 subunit C2 [ Homo sapiens (human) ]

Gene ID: 245973, updated on 3-Apr-2024

Summary

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Official Symbol
ATP6V1C2provided by HGNC
Official Full Name
ATPase H+ transporting V1 subunit C2provided by HGNC
Primary source
HGNC:HGNC:18264
See related
Ensembl:ENSG00000143882 MIM:618070; AllianceGenome:HGNC:18264
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VMA5; ATP6C2
Summary
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A,three B, and two G subunits, as well as a C, D, E, F, and H subunit. The V1 domain contains the ATP catalytic site. This gene encodes alternate transcriptional splice variants, encoding different V1 domain C subunit isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 47.0), skin (RPKM 40.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p25.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10720943..10785110)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10750978..10815109)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10861756..10925236)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10715723-10716922 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:10729319-10730518 Neighboring gene nucleolar protein 10 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:10794082-10795281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15310 Neighboring gene RNA, 7SL, cytoplasmic 832, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10877794-10877974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15311 Neighboring gene RNA, U7 small nuclear 138 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10898976-10899556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10905519-10906056 Neighboring gene uncharacterized LOC105373428 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10911826-10911981 Neighboring gene protein disulfide isomerase family A member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11166 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:10959839-10961038 Neighboring gene RNA, U7 small nuclear 176 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10971256-10971756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10975391-10975891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10979932-10980432 Neighboring gene uncharacterized LOC124905973

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Whole exome sequencing identified ATP6V1C2 as a novel candidate gene for recessive distal renal tubular acidosis. Jobst-Schwan T, et al. Kidney Int, 2020 Mar. PMID 31959358, Free PMC Article
  2. Multi-cancer V-ATPase molecular signatures: A distinctive balance of subunit C isoforms in esophageal carcinoma. Couto-Vieira J, et al. EBioMedicine, 2020 Jan. PMID 31901859, Free PMC Article
  3. Expression, purification and characterization of isoforms of peripheral stalk subunits of human V-ATPase. Rahman S, et al. Protein Expr Purif, 2011 Aug. PMID 21356312
  4. Structural features and nucleotide-binding capability of the C subunit are integral to the regulation of the eukaryotic V1Vo ATPases. Grüber G. Biochem Soc Trans, 2005 Aug. PMID 16042619
  5. Molecular cloning and characterization of novel tissue-specific isoforms of the human vacuolar H(+)-ATPase C, G and d subunits, and their evaluation in autosomal recessive distal renal tubular acidosis. Smith AN, et al. Gene, 2002 Sep 4. PMID 12384298

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Whole exome sequencing identified ATP6V1C2 as a novel candidate gene for recessive distal renal tubular acidosis.
    Title: Whole exome sequencing identified ATP6V1C2 as a novel candidate gene for recessive distal renal tubular acidosis.
  2. Multi-cancer V-ATPase molecular signatures: A distinctive balance of subunit C isoforms in esophageal carcinoma.
    Title: Multi-cancer V-ATPase molecular signatures: A distinctive balance of subunit C isoforms in esophageal carcinoma.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Association of genome-wide variation with highly sensitive cardiac troponin-T levels in European Americans and Blacks: a meta-analysis from atherosclerosis risk in communities and cardiovascular health studies.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables proton-transporting ATPase activity, rotational mechanism IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in positive regulation of Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in lysosomal membrane HDA PubMed 
part_of vacuolar proton-transporting V-type ATPase, V1 domain IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
V-type proton ATPase subunit C 2
Names
ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2
V-ATPase C2 subunit
vacuolar proton pump subunit C 2
NP_001034451.1
NP_001397636.1
NP_653184.2
XP_011508642.1
XP_011508643.1
XP_016859234.1
XP_047299813.1
XP_047299814.1
XP_047299815.1
XP_047299816.1
XP_047299817.1
XP_047299818.1
XP_047299819.1
XP_047299820.1
XP_054197221.1
XP_054197222.1
XP_054197223.1
XP_054197224.1
XP_054197225.1
XP_054197226.1
XP_054197227.1
XP_054197228.1
XP_054197229.1
XP_054197230.1
XP_054197231.1
XP_054197232.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050575.1 RefSeqGene

    Range
    5657..69137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001039362.2 → NP_001034451.1  V-type proton ATPase subunit C 2 isoform a

    See identical proteins and their annotated locations for NP_001034451.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC092687, AY039759, BC012142, BX358022, DB230703
    Consensus CDS
    CCDS42653.1
    UniProtKB/Swiss-Prot
    Q8NEY4, Q96EL8
    UniProtKB/TrEMBL
    A8KA87
    Related
    ENSP00000272238.4, ENST00000272238.9
    Conserved Domains (2) summary
    cd14785
    Location:55 → 75
    V-ATPase_C; 3-helical coiled coil [structural motif]
    pfam03223
    Location:5 → 417
    V-ATPase_C; V-ATPase subunit C

  2. NM_001410707.1 → NP_001397636.1  V-type proton ATPase subunit C 2 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC092687
    Consensus CDS
    CCDS92714.1
    UniProtKB/TrEMBL
    A0A0U1RR16
    Related
    ENSP00000489280.1, ENST00000635370.1

  3. NM_144583.4 → NP_653184.2  V-type proton ATPase subunit C 2 isoform b

    See identical proteins and their annotated locations for NP_653184.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform b), compared to isoform a.
    Source sequence(s)
    AC092687, AY039759, BC012142, BX358022, DB230703
    Consensus CDS
    CCDS1674.1
    UniProtKB/TrEMBL
    A8KA87
    Related
    ENSP00000371077.3, ENST00000381661.3
    Conserved Domains (2) summary
    cd14785
    Location:55 → 75
    V-ATPase_C; 3-helical coiled coil [structural motif]
    pfam03223
    Location:5 → 371
    V-ATPase_C; V-ATPase subunit C

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    10720943..10785110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443860.1 → XP_047299816.1  V-type proton ATPase subunit C 2 isoform X5

  2. XM_047443858.1 → XP_047299814.1  V-type proton ATPase subunit C 2 isoform X1

  3. XM_017003745.3 → XP_016859234.1  V-type proton ATPase subunit C 2 isoform X3

    UniProtKB/Swiss-Prot
    Q8NEY4, Q96EL8
    UniProtKB/TrEMBL
    A8KA87
    Related
    ENSP00000497038.1, ENST00000648362.1
    Conserved Domains (2) summary
    cd14785
    Location:55 → 75
    V-ATPase_C; 3-helical coiled coil [structural motif]
    pfam03223
    Location:5 → 417
    V-ATPase_C; V-ATPase subunit C

  4. XM_011510340.4 → XP_011508642.1  V-type proton ATPase subunit C 2 isoform X4

    See identical proteins and their annotated locations for XP_011508642.1

    UniProtKB/TrEMBL
    A8KA87
    Conserved Domains (2) summary
    cd14785
    Location:55 → 75
    V-ATPase_C; 3-helical coiled coil [structural motif]
    pfam03223
    Location:5 → 381
    V-ATPase_C; V-ATPase subunit C

  5. XM_047443857.1 → XP_047299813.1  V-type proton ATPase subunit C 2 isoform X1

  6. XM_047443859.1 → XP_047299815.1  V-type proton ATPase subunit C 2 isoform X2

  7. XM_011510341.3 → XP_011508643.1  V-type proton ATPase subunit C 2 isoform X9

    Conserved Domains (2) summary
    cd14785
    Location:55 → 75
    V-ATPase_C; 3-helical coiled coil [structural motif]
    pfam03223
    Location:5 → 222
    V-ATPase_C; V-ATPase subunit C

  8. XM_047443861.1 → XP_047299817.1  V-type proton ATPase subunit C 2 isoform X6

  9. XM_047443862.1 → XP_047299818.1  V-type proton ATPase subunit C 2 isoform X6

  10. XM_047443863.1 → XP_047299819.1  V-type proton ATPase subunit C 2 isoform X7

  11. XM_047443864.1 → XP_047299820.1  V-type proton ATPase subunit C 2 isoform X8

RNA

  1. XR_922661.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    10750978..10815109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341252.1 → XP_054197227.1  V-type proton ATPase subunit C 2 isoform X5

  2. XM_054341246.1 → XP_054197221.1  V-type proton ATPase subunit C 2 isoform X1

  3. XM_054341257.1 → XP_054197232.1  V-type proton ATPase subunit C 2 isoform X9

  4. XM_054341249.1 → XP_054197224.1  V-type proton ATPase subunit C 2 isoform X10

    UniProtKB/TrEMBL
    A0A0U1RR16

  5. XM_054341251.1 → XP_054197226.1  V-type proton ATPase subunit C 2 isoform X4

  6. XM_054341250.1 → XP_054197225.1  V-type proton ATPase subunit C 2 isoform X3

    UniProtKB/Swiss-Prot
    Q8NEY4, Q96EL8

  7. XM_054341247.1 → XP_054197222.1  V-type proton ATPase subunit C 2 isoform X1

  8. XM_054341248.1 → XP_054197223.1  V-type proton ATPase subunit C 2 isoform X2

  9. XM_054341253.1 → XP_054197228.1  V-type proton ATPase subunit C 2 isoform X6

  10. XM_054341254.1 → XP_054197229.1  V-type proton ATPase subunit C 2 isoform X6

  11. XM_054341255.1 → XP_054197230.1  V-type proton ATPase subunit C 2 isoform X7

  12. XM_054341256.1 → XP_054197231.1  V-type proton ATPase subunit C 2 isoform X8

RNA

  1. XR_008486310.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NEY4.2 GenPept UniProtKB/Swiss-Prot:Q8NEY4

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