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

Summary

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ATP5D Is a Potential Biomarker for Male Fertility.
Title: ATP5D Is a Potential Biomarker for Male Fertility.
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.
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.
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.

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

sY3084 (e-PCR)
- UniSTS:515126

D11S3114 (e-PCR)
- UniSTS:152207

RH80863 (e-PCR)
- UniSTS:87265

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 more info	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

EC 3.6.1.14

NP_001678.1

EC 3.6.1.14

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)

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
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