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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
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Genomic context

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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
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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

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