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    ATP5F1D ATP synthase F1 subunit delta [ Homo sapiens (human) ]

    Gene ID: 513, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ATP5F1Dprovided by HGNC
    Official Full Name
    ATP synthase F1 subunit deltaprovided by HGNC
    Primary source
    HGNC:HGNC:837
    See related
    Ensembl:ENSG00000099624 MIM:603150; AllianceGenome:HGNC:837
    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
    ATP5D; MC5DN5
    Summary
    This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the delta subunit of the catalytic core. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 30.9), colon (RPKM 30.8) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See ATP5F1D in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1241751..1244825)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1210310..1213384)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1241750..1244824)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9670 Neighboring gene Sharpr-MPRA regulatory region 13808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1208870-1209555 Neighboring gene serine/threonine kinase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1210982-1211768 Neighboring gene serine/threonine kinase 11 intron 1 Alu-mediated recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13596 Neighboring gene Sharpr-MPRA regulatory region 9448 Neighboring gene serine/threonine kinase 11 intron 3 Alu-mediated recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13597 Neighboring gene CACN subunit beta associated regulatory protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1239955-1240513 Neighboring gene CBARP divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1245978-1246723 Neighboring gene uncharacterized LOC102723811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9675 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1248659-1249192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9677 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1251037-1251976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9688 Neighboring gene midnolin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13601

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning of an import precursor of the delta-subunit of the human mitochondrial ATP synthase complex. Jordan EM, et al. Biochim Biophys Acta, 1992 Feb 28. PMID 1531933
    2. Role of copper in mitochondrial biogenesis via interaction with ATP synthase and cytochrome c oxidase. Medeiros DM, et al. J Bioenerg Biomembr, 2002 Oct. PMID 12539966
    3. Proteomic profiling of the spinal cord in ALS: decreased ATP5D levels suggest synaptic dysfunction in ALS pathogenesis. Engelen-Lee J, et al. Amyotroph Lateral Scler Frontotemporal Degener, 2017 May. PMID 27899032
    4. RNA m(1)A methylation regulates glycolysis of cancer cells through modulating ATP5D. Wu Y, et al. Proc Natl Acad Sci U S A, 2022 Jul 12. PMID 35867754, Free PMC Article
    5. F1-ATPase is a highly efficient molecular motor that rotates with discrete 120 degree steps. Yasuda R, et al. Cell, 1998 Jun 26. PMID 9657145

    See all (80) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ATP5D Is a Potential Biomarker for Male Fertility.
      Title: ATP5D Is a Potential Biomarker for Male Fertility.
    2. RNA m(1)A methylation regulates glycolysis of cancer cells through modulating ATP5D.
      Title: RNA m(1)A methylation regulates glycolysis of cancer cells through modulating ATP5D.
    3. These data establish c.245C>T (p.Pro82Leu) and c.317T>G (p.Val106Gly) in ATP5F1D as pathogenic variants leading to a Mendelian mitochondrial disease featuring episodic metabolic decompensation.
      Title: Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder.
    4. Immunohistochemical and immunofluorescent double staining of ATP5D and synaptophysin showed that the reduction of ATP5D was most pronounced at synapses in amyotrophic lateral sclerosis
      Title: Proteomic profiling of the spinal cord in ALS: decreased ATP5D levels suggest synaptic dysfunction in ALS pathogenesis.
    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

    Associated conditions

    Description Tests
    Mitochondrial complex 5 (ATP synthase) deficiency nuclear type 5
    MedGen: C4748269 OMIM: 618120 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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of ATP synthase, F1 complex, delta subunit (ATP5D) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit (ATP5D) 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
    contributes_to ADP binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    contributes_to ATP binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 aerobic respiration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial proton-transporting ATP synthase complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 motive force-driven mitochondrial ATP synthesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in proton transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to copper ion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proton-transporting ATP synthase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of proton-transporting ATP synthase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proton-transporting ATP synthase complex, catalytic core F(1) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of proton-transporting ATP synthase complex, catalytic core F(1) NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATP synthase subunit delta, mitochondrial
    Names
    ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit
    F-ATPase delta subunit
    mitochondrial ATP synthase complex delta-subunit precusor
    mitochondrial ATP synthase, delta subunit
    NP_001001975.1
    NP_001678.1

    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_001001975.2 → NP_001001975.1  ATP synthase subunit delta, mitochondrial precursor

      See identical proteins and their annotated locations for NP_001001975.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment in the 3' UTR, compared to variant 1. Both variants encode the same isoform.
      Source sequence(s)
      BC018817, X63423
      Consensus CDS
      CCDS12058.1
      UniProtKB/Swiss-Prot
      D6W5Y3, P30049, Q6FG90
      Related
      ENSP00000378995.1, ENST00000395633.5
      Conserved Domains (1) summary
      cd12152
      Location:38 → 162
      F1-ATPase_delta; mitochondrial ATP synthase delta subunit

    2. NM_001687.5 → NP_001678.1  ATP synthase subunit delta, mitochondrial precursor

      See identical proteins and their annotated locations for NP_001678.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants encode the same isoform.
      Source sequence(s)
      BC018817, X63422
      Consensus CDS
      CCDS12058.1
      UniProtKB/Swiss-Prot
      D6W5Y3, P30049, Q6FG90
      Related
      ENSP00000215375.1, ENST00000215375.7
      Conserved Domains (1) summary
      cd12152
      Location:38 → 162
      F1-ATPase_delta; mitochondrial ATP synthase delta subunit

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      1241751..1244825
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      1210310..1213384
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P30049.2 GenPept UniProtKB/Swiss-Prot:P30049

    Gene LinkOut

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

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