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

Gene ID: 513, updated on 5-Mar-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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Location:
19p13.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1241751..1244825)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1210310..1213384)
105.20220307 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

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. 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
  2. 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
  3. 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
  4. 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
  5. ATP5D Is a Potential Biomarker for Male Fertility. Wang YB, et al. Oxid Med Cell Longev, 2023. PMID 36686378, Free PMC Article

See all (69) 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
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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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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
  
part_of mitochondrial proton-transporting ATP synthase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of mitochondrial proton-transporting ATP synthase complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrion 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_2023_10

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

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