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

    Gene ID: 245973, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See ATP6V1C2 in Genome Data Viewer
    Location:
    2p25.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (10720943..10785110)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10750978..10815109)
    RS_2024_09 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 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. 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
    4. 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
    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 (32) 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 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_2024_08

    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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