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    ATP5PD ATP synthase peripheral stalk subunit d [ Homo sapiens (human) ]

    Gene ID: 10476, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ATP5PDprovided by HGNC
    Official Full Name
    ATP synthase peripheral stalk subunit dprovided by HGNC
    Primary source
    HGNC:HGNC:845
    See related
    Ensembl:ENSG00000167863 MIM:618121; AllianceGenome:HGNC:845
    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
    ATPQ; APT5H; ATP5H
    Summary
    Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the d subunit of the Fo complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. In addition, three pseudogenes are located on chromosomes 9, 12 and 15. [provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in heart (RPKM 220.3), kidney (RPKM 160.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See ATP5PD in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75038863..75046969, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (75930610..75938401, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73034958..73043064, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73029803-73030784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8952 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73031872-73032031 Neighboring gene tRNA-Arg (anticodon CCT) 2-1 Neighboring gene tRNA-Arg (anticodon TCG) 3-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73037362-73037932 Neighboring gene potassium channel tetramerization domain containing 2 Neighboring gene RNA, 7SL, cytoplasmic 573, pseudogene Neighboring gene Sharpr-MPRA regulatory region 3986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12732 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73074528-73075727 Neighboring gene tripartite motif containing 80, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089299-73089872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089873-73090445 Neighboring gene solute carrier family 16 member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73100784-73101284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73101285-73101785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8955 Neighboring gene armadillo repeat containing 7

    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. The complete amino acid sequence of subunit d of rat liver mitochondrial H(+)-ATP synthase. Higuti T, et al. J Biochem, 1993 Nov. PMID 7509337
    2. Mitochondrial reprogramming via ATP5H loss promotes multimodal cancer therapy resistance. Song KH, et al. J Clin Invest, 2018 Aug 31. PMID 30124467, Free PMC Article
    3. Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males. Katz Shroitman N, et al. J Psychiatr Res, 2023 Feb. PMID 36640659
    4. ATP5H/KCTD2 locus is associated with Alzheimer's disease risk. Boada M, et al. Mol Psychiatry, 2014 Jun. PMID 23857120, Free PMC Article
    5. Systems biology approach to late-onset Alzheimer's disease genome-wide association study identifies novel candidate genes validated using brain expression data and Caenorhabditis elegans experiments. Mukherjee S, et al. Alzheimers Dement, 2017 Oct. PMID 28242297, Free PMC Article

    See all (112) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males.
      Title: Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males.
    2. ATP5H loss in the tumor is strongly linked to failure of therapy, disease progression, and poor survival in patients with cancer.
      Title: Mitochondrial reprogramming via ATP5H loss promotes multimodal cancer therapy resistance.
    3. The Network analyses identified ATP5H expression in temporal cortex in patient with late-onset Alzheimer's disease.
      Title: Systems biology approach to late-onset Alzheimer's disease genome-wide association study identifies novel candidate genes validated using brain expression data and Caenorhabditis elegans experiments.
    4. By merging results of a meta-GWAS, results in the CHARGE consortium data sets and an in vivo genotyping comprising 4501 individuals, detected a novel locus ATP5H/KCTD2 associated with Alzheimer's disease risk
      Title: ATP5H/KCTD2 locus is associated with Alzheimer's disease risk.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    6. This protein has been found differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia.
      Title: Proteomic analysis of dorsolateral prefrontal cortex indicates the involvement of cytoskeleton, oligodendrocyte, energy metabolism and new potential markers in schizophrenia.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d (ATP5H) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    contributes_to proton-transporting ATP synthase activity, rotational mechanism IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to proton-transporting ATP synthase activity, rotational mechanism IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proton motive force-driven ATP synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proton motive force-driven ATP synthesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in proton motive force-driven mitochondrial ATP synthesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    part_of proton-transporting ATP synthase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of proton-transporting ATP synthase complex, coupling factor F(o) IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ATP synthase subunit d, mitochondrial
    Names
    ATP synthase D chain, mitochondrial
    ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d
    ATP synthase, H+ transporting, mitochondrial F1F0, subunit d
    ATP synthase, H+ transporting, mitochondrial Fo complex subunit D
    ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d
    ATPase subunit d
    My032 protein
    NP_001003785.1
    NP_006347.1

    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.

    mRNA and Protein(s)

    1. NM_001003785.2 → NP_001003785.1  ATP synthase subunit d, mitochondrial isoform b

      See identical proteins and their annotated locations for NP_001003785.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (b), that is missing an internal segment compared to isoform a.
      Source sequence(s)
      AA608885, BC032245
      Consensus CDS
      CCDS32727.1
      UniProtKB/Swiss-Prot
      O75947
      Related
      ENSP00000344230.4, ENST00000344546.8
      Conserved Domains (1) summary
      pfam05873
      Location:3 → 131
      Mt_ATP-synt_D; ATP synthase D chain, mitochondrial (ATP5H)

    2. NM_006356.3 → NP_006347.1  ATP synthase subunit d, mitochondrial isoform a

      See identical proteins and their annotated locations for NP_006347.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript, and it encodes the longer isoform a.
      Source sequence(s)
      AA608885, BC029392, BC032245, BC038092
      Consensus CDS
      CCDS11712.1
      UniProtKB/Swiss-Prot
      B2R5L6, O75947, Q9H3J4
      Related
      ENSP00000301587.4, ENST00000301587.9
      Conserved Domains (1) summary
      pfam05873
      Location:3 → 155
      Mt_ATP-synt_D; ATP synthase D chain, mitochondrial (ATP5H)

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      75038863..75046969 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      75930610..75938401 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75947.3 GenPept UniProtKB/Swiss-Prot:O75947

    Gene LinkOut

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