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    ATP6AP1 ATPase H+ transporting accessory protein 1 [ Homo sapiens (human) ]

    Gene ID: 537, updated on 11-Apr-2024

    Summary

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    Official Symbol
    ATP6AP1provided by HGNC
    Official Full Name
    ATPase H+ transporting accessory protein 1provided by HGNC
    Primary source
    HGNC:HGNC:868
    See related
    Ensembl:ENSG00000071553 MIM:300197; AllianceGenome:HGNC:868
    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
    16A; CF2; Ac45; XAP3; XAP-3; ATP6S1; VATPS1; ATP6IP1
    Summary
    This gene encodes a component of a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Vacuolar ATPase (V-ATPase) is comprised of a cytosolic V1 (site of the ATP catalytic site) and a transmembrane V0 domain. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. The encoded protein of this gene may assist in the V-ATPase-mediated acidification of neuroendocrine secretory granules. This protein may also play a role in early development. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in brain (RPKM 59.1), thyroid (RPKM 48.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATP6AP1 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154428677..154436516)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152665185..152673024)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153657023..153664862)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene deoxyribonuclease 1 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21101 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153641748-153641921 Neighboring gene tafazzin, phospholipid-lysophospholipid transacylase Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153647927-153648428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153648429-153648928 Neighboring gene ATP6AP1 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153656739-153657240 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153665032-153665532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153666887-153667386 Neighboring gene GDP dissociation inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153672115-153672682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153673251-153673818 Neighboring gene family with sequence similarity 50 member A Neighboring gene microRNA 6858

    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. Expanding the phenotype of ATP6AP1 deficiency. Barua S, et al. Cold Spring Harb Mol Case Stud, 2022 Jun. PMID 35732497, Free PMC Article
    2. Prognostic and immunological value of ATP6AP1 in breast cancer: implications for SARS-CoV-2. Wang J, et al. Aging (Albany NY), 2021 Jul 6. PMID 34228637, Free PMC Article
    3. Severe phenotype of ATP6AP1-CDG in two siblings with a novel mutation leading to a differential tissue-specific ATP6AP1 protein pattern, cellular oxidative stress and hepatic copper accumulation. Ondruskova N, et al. J Inherit Metab Dis, 2020 Jul. PMID 32216104, Free PMC Article
    4. Prenatal and postnatal phenotype of a pathologic variant in the ATP6AP1 gene. Tvina A, et al. Eur J Med Genet, 2020 Jun. PMID 32058063
    5. Expanding the phenotype of metabolic cutis laxa with an additional disorder of N-linked protein glycosylation. Witters P, et al. Eur J Hum Genet, 2018 May. PMID 29192153, Free PMC Article

    See all (100) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATP6AP1 as a potential prognostic biomarker in CRC by comprehensive analysis and verification.
      Title: ATP6AP1 as a potential prognostic biomarker in CRC by comprehensive analysis and verification.
    2. Expanding the phenotype of ATP6AP1 deficiency.
      Title: Expanding the phenotype of ATP6AP1 deficiency.
    3. SARS-CoV-2 non-structural protein 6 triggers NLRP3-dependent pyroptosis by targeting ATP6AP1.
      Title: SARS-CoV-2 non-structural protein 6 triggers NLRP3-dependent pyroptosis by targeting ATP6AP1.
    4. Severe phenotype of ATP6AP1-CDG in two siblings with a novel mutation leading to a differential tissue-specific ATP6AP1 protein pattern, cellular oxidative stress and hepatic copper accumulation.
      Title: Severe phenotype of ATP6AP1-CDG in two siblings with a novel mutation leading to a differential tissue-specific ATP6AP1 protein pattern, cellular oxidative stress and hepatic copper accumulation.
    5. Prognostic and immunological value of ATP6AP1 in breast cancer: implications for SARS-CoV-2.
      Title: Prognostic and immunological value of ATP6AP1 in breast cancer: implications for SARS-CoV-2.
    6. Prenatal and postnatal phenotype of a pathologic variant in the ATP6AP1 gene.
      Title: Prenatal and postnatal phenotype of a pathologic variant in the ATP6AP1 gene.
    7. Here we report on the previously unreported finding of CL due to a hemizygous mutation in the gene ATP6AP1 (MIM 300972), a component of the V-ATPase complex that was recently described to cause an X-linked N-glycosylation disorder with liver disease
      Title: Expanding the phenotype of metabolic cutis laxa with an additional disorder of N-linked protein glycosylation.
    8. inactivating mutations of ATP6AP1 are likely oncogenic drivers of Granular cell tumors;a genetic link between endosomal pH regulation and tumorigenesis
      Title: Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors.
    9. Data indicate V-ATPase Ac45 subunit assembly with immunoglobulin production and cognitive function.
      Title: ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation.
    10. ATP6AP1 is somatically mutated in 12% of follicular lymphoma tumors. Mutations clustered around the transmembrane domain.
      Title: Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    Associated conditions

    Description Tests
    Immunodeficiency 47
    MedGen: C4310819 OMIM: 300972 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of ATP6AP1 by shRNA significantly inhibits HIV-1 replication in CD4+ T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies ATP6AP1, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC129781

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transporter activator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to increased oxygen levels IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosomal lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosome to plasma membrane protein transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intracellular iron ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular pH reduction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in lysosomal lumen acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in osteoclast development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proton transmembrane transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of cellular pH IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle lumen acidification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vacuolar acidification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in clathrin-coated vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proton-transporting V-type ATPase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of proton-transporting V-type ATPase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proton-transporting two-sector ATPase complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    V-type proton ATPase subunit S1
    Names
    ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1
    ATPase, H+ transporting, lysosomal accessory protein 1
    ATPase, H+ transporting, lysosomal interacting protein 1
    H-ATPase subunit
    V-ATPase Ac45 subunit
    V-ATPase S1 accessory protein
    V-ATPase subunit S1
    X-associated protein 3
    epididymis secretory sperm binding protein
    protein XAP-3
    vacuolar ATPase subunit S1
    vacuolar proton pump subunit S1
    NP_001174.2

    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_052807.1 RefSeqGene

      Range
      5046..12885
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001183.6 → NP_001174.2  V-type proton ATPase subunit S1 precursor

      See identical proteins and their annotated locations for NP_001174.2

      Status: REVIEWED

      Source sequence(s)
      AK075284, AK289452
      Consensus CDS
      CCDS35451.1
      UniProtKB/Swiss-Prot
      A6ZKI4, Q15904, Q8NBT4, Q9H0C7
      UniProtKB/TrEMBL
      A0A384MQW4, B3KR70
      Related
      ENSP00000358777.2, ENST00000369762.7
      Conserved Domains (1) summary
      pfam05827
      Location:321 → 468
      ATP-synt_S1; Vacuolar ATP synthase subunit S1 (ATP6S1)

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      154428677..154436516
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152665185..152673024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15904.2 GenPept UniProtKB/Swiss-Prot:Q15904

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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