ATP5F1D Gene (Protein Coding)

ATP Synthase F1 Subunit Delta

GC19P001242
GIFtS:
34
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 c... See more...

Aliases for ATP5F1D Gene

Aliases for ATP5F1D Gene

  • ATP Synthase F1 Subunit Delta 2 3 4 5
  • ATP Synthase, H+ Transporting, Mitochondrial F1 Complex, Delta Subunit 2 3
  • ATP Synthase Subunit Delta, Mitochondrial 3 4
  • F-ATPase Delta Subunit 3 4
  • ATP5D 3 4
  • Mitochondrial ATP Synthase Complex Delta-Subunit Precusor 3
  • Mitochondrial ATP Synthase, Delta Subunit 3
  • ATP5F1D 5
  • MC5DN5 3

External Ids for ATP5F1D Gene

Previous HGNC Symbols for ATP5F1D Gene

  • ATP5D

Summaries for ATP5F1D Gene

Entrez Gene Summary for ATP5F1D Gene

  • 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]

GeneCards Summary for ATP5F1D Gene

ATP5F1D (ATP Synthase F1 Subunit Delta) is a Protein Coding gene. Diseases associated with ATP5F1D include Mitochondrial Complex V Deficiency, Nuclear Type 5 and Isolated Atp Synthase Deficiency. Among its related pathways are Pathways of neurodegeneration - multiple diseases and purine nucleotides de novo biosynthesis.

UniProtKB/Swiss-Prot Summary for ATP5F1D Gene

  • Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain (PubMed:29478781). F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP turnover in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(1) domain and of the central stalk which is part of the complex rotary element. Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits (PubMed:1531933).

Gene Wiki entry for ATP5F1D Gene

Additional gene information for ATP5F1D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP5F1D Gene

Genomics for ATP5F1D Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ATP5F1D Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP5F1D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP5F1D

Genomic Locations for ATP5F1D Gene

Latest Assembly
chr19:1,241,746-1,244,825
(GRCh38/hg38)
Size:
3,080 bases
Orientation:
Plus strand

Previous Assembly
chr19:1,241,750-1,244,824
(GRCh37/hg19 by Entrez Gene)
Size:
3,075 bases
Orientation:
Plus strand

chr19:1,241,749-1,244,824
(GRCh37/hg19 by Ensembl)
Size:
3,076 bases
Orientation:
Plus strand

Genomic View for ATP5F1D Gene

Genes around ATP5F1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP5F1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP5F1D Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATP5F1D Gene

Proteins for ATP5F1D Gene

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  • Protein details for ATP5F1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P30049-ATPD_HUMAN
    Recommended name:
    ATP synthase subunit delta, mitochondrial
    Protein Accession:
    P30049
    Secondary Accessions:
    • D6W5Y3
    • Q6FG90

    Protein attributes for ATP5F1D Gene

    Size:
    168 amino acids
    Molecular mass:
    17490 Da
    Quaternary structure:
    • F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) seems to have nine subunits: a, b, c, d, e, f, g, F6 and 8 (or A6L). Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MD and ATP5MPL (By similarity).

neXtProt entry for ATP5F1D Gene

Post-translational modifications for ATP5F1D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATP5F1D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ATP5F1D Gene

Domains & Families for ATP5F1D Gene

Gene Families for ATP5F1D Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ATP5F1D Gene

InterPro:
Blocks:
  • H+-transporting two-sector ATPase, delta/epsilon subunit

Suggested Antigen Peptide Sequences for ATP5F1D Gene

GenScript: Design optimal peptide antigens:
  • F-ATPase delta subunit (ATPD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P30049

UniProtKB/Swiss-Prot:

ATPD_HUMAN :
  • Belongs to the ATPase epsilon chain family.
Family:
  • Belongs to the ATPase epsilon chain family.
genes like me logo Genes that share domains with ATP5F1D: view

Function for ATP5F1D Gene

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Molecular function for ATP5F1D Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain (PubMed:29478781). F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP turnover in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(1) domain and of the central stalk which is part of the complex rotary element. Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits (PubMed:1531933).

Phenotypes From GWAS Catalog for ATP5F1D Gene

Gene Ontology (GO) - Molecular Function for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 28514442
GO:0005524 contributes_to ATP binding NAS 12539966
GO:0016887 ATPase activity NAS 12539966
GO:0043531 contributes_to ADP binding NAS 12539966
GO:0046933 contributes_to proton-transporting ATP synthase activity, rotational mechanism IEA,IDA 12110673
genes like me logo Genes that share ontologies with ATP5F1D: view
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Human Phenotype Ontology for ATP5F1D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP5F1D Gene

Localization for ATP5F1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP5F1D Gene

Mitochondrion. Mitochondrion inner membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP5F1D gene
Compartment Confidence
mitochondrion 5
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) IBA,NAS 12539966
GO:0005739 mitochondrion NAS 12887009
GO:0005743 mitochondrial inner membrane ISS --
GO:0005753 mitochondrial proton-transporting ATP synthase complex NAS 1531933
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with ATP5F1D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ATP5F1D Gene

Pathways & Interactions for ATP5F1D Gene

genes like me logo Genes that share pathways with ATP5F1D: view

Gene Ontology (GO) - Biological Process for ATP5F1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006119 oxidative phosphorylation NAS 12539966
GO:0006754 ATP biosynthetic process TAS --
GO:0006811 ion transport IEA --
GO:0009060 aerobic respiration IMP 29478781
GO:0015986 ATP synthesis coupled proton transport IEA,IBA 21873635
genes like me logo Genes that share ontologies with ATP5F1D: view

No data available for SIGNOR curated interactions for ATP5F1D Gene

Drugs & Compounds for ATP5F1D Gene

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(10) Drugs for ATP5F1D Gene - From: DrugBank, DGIdb, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Desflurane Approved Pharma Target, other/unknown, antagonist 226
Isoflurane Approved, Vet_approved Pharma Target, unknown 136
Enflurane Approved, Investigational, Vet_approved Pharma 2
Methoxyflurane Approved, Investigational, Vet_approved Pharma antagonist 23
Sevoflurane Approved, Vet_approved Pharma antagonist 797

(2) Additional Compounds for ATP5F1D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 58-64-0
trifluoroacetic acid
  • Acide trifluoroacetique
  • CF3COOH
  • Perfluoroacetic acid
  • TFA
  • Trifluoressigsaeure
 76-05-1
genes like me logo Genes that share compounds with ATP5F1D: view

Transcripts for ATP5F1D Gene

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mRNA/cDNA for ATP5F1D Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for ATP5F1D Gene

No ASD Table

Relevant External Links for ATP5F1D Gene

GeneLoc Exon Structure for
ATP5F1D

Expression for ATP5F1D Gene

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  1. Primer products for research

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP5F1D

Evidence on tissue expression from TISSUES for ATP5F1D Gene

  • Nervous system(4.7)
  • Liver(4.7)
  • Lung(4.3)
  • Muscle(4.2)
  • Heart(4)
  • Kidney(3.5)
  • Stomach(3.1)
  • Intestine(3)
  • Skin(2.3)
genes like me logo Genes that share expression patterns with ATP5F1D: view

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP5F1D Gene

Orthologs for ATP5F1D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ATP5F1D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ATP5D 29 30
  • 99.21 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ATP5D 29 30
  • 83.53 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia ATP5D 29 30
  • 83.33 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Atp5d 29
  • 80.56 (n)
Mouse
(Mus musculus)
 Mammalia Atp5d 29 16 30
  • 80.36 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia ATP5D 30
  • 78 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia ATP5D 30
  • 78 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves ATP5D 29 30
  • 76.53 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia ATP5D 30
  • 60 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia atp5d 29
  • 65.44 (n)
Str.10780 29
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23716 29
Zebrafish
(Danio rerio)
 Actinopterygii atp5d 29 30
  • 70.96 (n)
 OneToOne
wufk58f09 29
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.8822 29
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007841 29
  • 59.4 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta l(1)G0230 29 30
  • 55.39 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea F58F12.1 29 30
  • 49.62 (n)
 OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AEL008W 29
  • 52.42 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0F14773g 29
  • 45.48 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes ATP16 29 30 32
  • 43.17 (n)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT5G47030 29
  • 45.45 (n)
Rice
(Oryza sativa)
 Liliopsida Os07g0495200 29
  • 48.74 (n)
Bread mold
(Neurospora crassa)
 Ascomycetes NCU00385 29
  • 50.78 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.7960 30
  • 48 (a)
 OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes atp16 29
  • 42.49 (n)
Species where no ortholog for ATP5F1D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ATP5F1D Gene

ENSEMBL:
Gene Tree for ATP5F1D (if available)
TreeFam:
Gene Tree for ATP5F1D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATP5F1D: view image
Alliance of Genome Resources:
Additional Orthologs for ATP5F1D

Paralogs for ATP5F1D Gene

No data available for Paralogs for ATP5F1D Gene

Variants for ATP5F1D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP5F1D Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs155574598 Mitochondrial complex V deficiency, nuclear type 5 (MC5DN5) [MIM:618120] p.Val106Gly
rs1555745989 Pathogenic: Mitochondrial complex 5 (ATP synthase) deficiency nuclear type 5; Mitochondrial diseases 1,244,118(+) T/G
NM_001687.5(ATP5F1D):c.317T>G (p.Val106Gly) 		MISSENSE
rs867410737 Pathogenic: Decreased activity of mitochondrial ATP synthase complex; Mitochondrial complex 5 (ATP synthase) deficiency nuclear type 5. Mitochondrial complex V deficiency, nuclear type 5 (MC5DN5) [MIM:618120] 1,242,559(+) C/Tp.Pro82Leu
NM_001687.5(ATP5F1D):c.245C>T (p.Pro82Leu) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ATP5F1D Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ATP5F1D Gene

Variant ID Type Subtype PubMed ID
dgv136n111 CNV deletion 26073780
dgv6196n54 CNV loss 21841781
esv2758743 CNV gain+loss 17122850
nsv1058677 CNV loss 25217958
nsv1060536 CNV gain 25217958
nsv1160555 CNV deletion 26073780
nsv470103 CNV gain 18288195
nsv470104 CNV loss 18288195
nsv578268 CNV loss 21841781
nsv578272 CNV loss 21841781
nsv828368 CNV gain 20364138
nsv953941 CNV deletion 24416366
nsv9662 CNV gain 18304495

Variation tolerance for ATP5F1D Gene

Gene Damage Index Score: 1.20; 24.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP5F1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP5F1D
Leiden Open Variation Database (LOVD)
ATP5F1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATP5F1D Gene

Disorders for ATP5F1D Gene

MalaCards: The human disease database

(5) MalaCards diseases for ATP5F1D Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
mitochondrial complex v deficiency, nuclear type 5
  • mc5dn5
isolated atp synthase deficiency
  • isolated mitochondrial respiratory chain complex v deficiency
mitochondrial disorders
  • mitochondrial encephalomyopathies
3-methylglutaconic aciduria
  • 3-methyl glutaconic aciduria
complex partial epilepsy
  • complex partial epileptic seizure
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

ATPD_HUMAN
  • Mitochondrial complex V deficiency, nuclear type 5 (MC5DN5) [MIM:618120]: A mitochondrial disorder characterized by childhood onset of episodic metabolic decompensation featuring lactic acidosis and hyperammonemia accompanied by ketoacidosis or hypoglycemia. Chronic manifestations include developmental delay, easy fatiguability, and 3-methylglutaconic aciduria. The transmission pattern of MC5DN5 is consistent with autosomal recessive inheritance. {ECO:0000269 PubMed:29478781}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.

Additional Disease Information for ATP5F1D

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with ATP5F1D: view

No data available for Genatlas for ATP5F1D Gene

Publications for ATP5F1D Gene

  1. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. (PMID: 29478781) Oláhová M … Wheeler MT (American journal of human genetics 2018) 3 4 72
  2. Molecular cloning of an import precursor of the delta-subunit of the human mitochondrial ATP synthase complex. (PMID: 1531933) Jordan EM … Breen GA (Biochimica et biophysica acta 1992) 2 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4
  5. Human liver protein map: a reference database established by microsequencing and gel comparison. (PMID: 1286669) Hochstrasser DF … Vargas R (Electrophoresis 1992) 3 4

ExternalLinks

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