ATP5F1D

ATP synthase F1 subunit delta, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 19:1241746-1244825

Previous symbols: [ "ATP5D" ]

Links

ENSG00000099624 ∙ NCBI:513 ∙ OMIM:603150 ∙ HGNC:837 ∙ Uniprot:P30049 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial proton-transporting ATP synthase complex deficiency (Supportive), mode of inheritance: AR
• mitochondrial complex V (ATP synthase) deficiency, nuclear type 5 (Limited), mode of inheritance: AR
• mitochondrial complex V (ATP synthase) deficiency, nuclear type 5 (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5F1D gene.

• not_provided (120 variants)
• Inborn_genetic_diseases (41 variants)
• ATP5F1D-related_disorder (12 variants)
• Mitochondrial_complex_V_(ATP_synthase)_deficiency,_nuclear_type_5 (4 variants)
• Decreased_activity_of_mitochondrial_ATP_synthase_complex (1 variants)
• not_specified (1 variants)
• Mitochondrial_disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5F1D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001687.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	37	3	41
missense	2		72	6	1	81
nonsense			3			3
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	2	0	77	43	4

Highest pathogenic variant AF is 0.00000215354

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5F1D	protein_coding	protein_coding	ENST00000215375	4	3076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0738	0.758	124281	0	2	124283	0.00000805

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	82	93.4	0.878	0.00000586	1017
Missense in Polyphen		29	32.97	0.87958		330
Synonymous	0.451	45	49.0	0.918	0.00000377	375
Loss of Function	0.975	2	4.14	0.483	1.76e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000644	0.0000625
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000897	0.00000893
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. 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.
• Pathway: Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Doxorubicin Pathway (Cardiomyocyte Cell), Pharmacodynamics;Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Mitochondrial Electron Transport Chain;Electron Transport Chain;Oxidative phosphorylation;adenosine ribonucleotides <i>de novo</i> biosynthesis;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;superpathway of purine nucleotide salvage;Cristae formation;Mitochondrial biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;purine nucleotides <i>de novo</i> biosynthesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.625
• ghis: 0.613

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atp5d

Gene ontology

• Biological process: oxidative phosphorylation;ATP biosynthetic process;ATP synthesis coupled proton transport;cristae formation;mitochondrial ATP synthesis coupled proton transport;response to copper ion;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: mitochondrial proton-transporting ATP synthase complex, catalytic core F(1);mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex;mitochondrial matrix
• Molecular function: transporter activity;ATP binding;ATPase activity;transmembrane transporter activity;ADP binding;proton-transporting ATP synthase activity, rotational mechanism