Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	513
Gene name	ATP synthase F1 subunit delta
Gene symbol	ATP5F1D
Synonyms (NCBI Gene)	ATP5DMC5DN5
Chromosome	19
Chromosome location	19p13.3
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 lin

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs867410737	C>T	Pathogenic	Missense variant, coding sequence variant
rs1555745989	T>G	Pathogenic	Coding sequence variant, missense variant

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005198	Function	Structural molecule activity	IDA	29499186
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 32814053, 33961781
GO:0005524	Function	ATP binding	NAS	12539966
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IC	12110673
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	NAS	12887009
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005743	Component	Mitochondrial inner membrane	ISS
GO:0005743	Component	Mitochondrial inner membrane	NAS	26297831
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006754	Process	ATP biosynthetic process	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0009060	Process	Aerobic respiration	IMP	29478781
GO:0015986	Process	Proton motive force-driven ATP synthesis	IBA
GO:0015986	Process	Proton motive force-driven ATP synthesis	IEA
GO:0015986	Process	Proton motive force-driven ATP synthesis	NAS	26297831
GO:0016020	Component	Membrane	IEA
GO:0033615	Process	Mitochondrial proton-transporting ATP synthase complex assembly	IDA	29499186
GO:0033615	Process	Mitochondrial proton-transporting ATP synthase complex assembly	IMP	29478781
GO:0042776	Process	Proton motive force-driven mitochondrial ATP synthesis	IDA	12110673
GO:0042776	Process	Proton motive force-driven mitochondrial ATP synthesis	NAS	12539966
GO:0043531	Function	ADP binding	NAS	12539966
GO:0045259	Component	Proton-transporting ATP synthase complex	IBA
GO:0045259	Component	Proton-transporting ATP synthase complex	IDA	12110673, 37244256
GO:0045259	Component	Proton-transporting ATP synthase complex	IEA
GO:0045259	Component	Proton-transporting ATP synthase complex	NAS	1531933, 12539966, 26297831
GO:0046688	Process	Response to copper ion	NAS	12539966
GO:0046933	Function	Proton-transporting ATP synthase activity, rotational mechanism	IBA
GO:0046933	Function	Proton-transporting ATP synthase activity, rotational mechanism	IDA	12110673
GO:0046933	Function	Proton-transporting ATP synthase activity, rotational mechanism	IEA
GO:1902600	Process	Proton transmembrane transport	IEA

MIM	HGNC	e!Ensembl
603150	837	ENSG00000099624

P30049

Protein name

ATP synthase F(1) complex subunit delta, mitochondrial (ATP synthase F1 subunit delta) (F-ATPase delta subunit)

Protein function

Subunit delta, of the mitochondrial membrane ATP synthase complex (F(1)F(0) ATP synthase or Complex V) that produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the

PDB

8H9F , 8H9J , 8H9M , 8H9Q , 8H9S , 8H9T , 8H9U , 8H9V , 8KHF , 8KI3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02823	ATP-synt_DE_N	38 → 119	ATP synthase, Delta/Epsilon chain, beta-sandwich domain	Domain

Sequence

MLPAALLRRPGLGRLVRHARAYAEAAAAPAAASGPNQMSFTFASPTQVFFNGANVRQVDV
PTLTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSIAVNADSSVQLLAEEAV
TLDMLDLGAAKANLEKAQAELVGTADEATRAEIQIRIEANEALVKALE

Sequence length

168

Interactions

View interactions

	KEGG		Reactome
	Oxidative phosphorylation Metabolic pathways Thermogenesis Alzheimer disease Parkinson disease Amyotrophic lateral sclerosis Huntington disease Prion disease Pathways of neurodegeneration - multiple diseases Chemical carcinogenesis - reactive oxygen species Diabetic cardiomyopathy		Formation of ATP by chemiosmotic coupling Cristae formation

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Decreased activity of mitochondrial ATP synthase complex	Pathogenic	rs867410737	RCV000541368	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mitochondrial complex V (ATP synthase) deficiency, nuclear type 5	Pathogenic	rs867410737, rs1555745989	RCV000680226 RCV000680227	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mitochondrial disease	Pathogenic	rs1555745989	RCV000627809	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ATP5F1D-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL COMPLEX V DEFICIENCY, NUCLEAR TYPE 5	—	ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO ClinVar, Disgenet, GWAS catalog, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URINARY BLADDER NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (35)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	12114434		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	24558171	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	CTD_human_DG	26039340		★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	29478781	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	27899032	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Failure	Heart failure	Pubtator	29478781	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intermittent lactic acidemia	Intermittent lactic acidemia	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Isolated ATP synthase deficiency	Isolated ATP Synthase Deficiency	ORPHANET_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Isolated ATP synthase deficiency	Isolated ATP Synthase Deficiency	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ketosis	Ketosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Left-Sided Heart Failure	Heart Failure	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Neoplasms	Liver neoplasm	Pubtator	27899032	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	CTD_human_DG	26039340		★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
MITOCHONDRIAL COMPLEX V (ATP SYNTHASE) DEFICIENCY, NUCLEAR TYPE 5	Mitochondrial Complex Deficiency	UNIPROT_DG	29478781		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MITOCHONDRIAL COMPLEX V (ATP SYNTHASE) DEFICIENCY, NUCLEAR TYPE 5	Mitochondrial Complex Deficiency	GENOMICS_ENGLAND_DG	29478781		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MITOCHONDRIAL COMPLEX V (ATP SYNTHASE) DEFICIENCY, NUCLEAR TYPE 5	Mitochondrial Complex Deficiency	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Mitochondrial Diseases	Mitochondrial Diseases	BEFREE	29478781		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial Diseases	CLINVAR_DG	29478781		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial disease	Pubtator	29478781	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mongolian Spot	Mongolian Spot	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neonatal hypoglycemia	Hypoglycemia	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nevus	Nevus	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Night blindness congenital stationary	Night blindness, congenital stationary	Pubtator	27899032	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Oxidative Phosphorylation Deficiencies	Oxidative Phosphorylation Deficiency	BEFREE	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	CLINVAR_DG	29478781		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37482618	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

ATP5F1D (ATP synthase F1 subunit delta)