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 5 (ATP synthase) deficiency nuclear type 5 (Limited), mode of inheritance: AR
• mitochondrial complex 5 (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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				29	3	32
missense			64	3	1	68
nonsense			3			3
start loss						0
frameshift			1			1
inframe indel			4			4
splice donor/acceptor (+/-2bp)						0
splice region			3	2		5
non coding				9	4	13
Total	0	0	72	41	8

Variants in ATP5F1D

This is a list of pathogenic ClinVar variants found in the ATP5F1D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-1241837-C-CGCCCGCCGCTGCCATGCT		Inborn genetic diseases	Uncertain significance (Oct 26, 2023)
19-1241841-C-T		ATP5F1D-related disorder	Likely benign (May 03, 2021)
19-1241859-C-T			Likely benign (Apr 29, 2024)
19-1241863-G-A		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)
19-1241866-C-G			Uncertain significance (Oct 19, 2022)
19-1241872-C-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2023)
19-1241875-C-T		Mitochondrial complex 5 (ATP synthase) deficiency nuclear type 5 • ATP5F1D-related disorder	Conflicting classifications of pathogenicity (Jan 23, 2025)
19-1241876-G-C			Uncertain significance (Jun 14, 2022)
19-1241880-G-T			Likely benign (Jun 01, 2024)
19-1241890-C-T			Uncertain significance (May 30, 2023)
19-1241895-C-A			Likely benign (Jun 28, 2022)
19-1241895-C-T			Likely benign (Nov 29, 2022)
19-1241896-G-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2024)
19-1241901-C-T			Likely benign (May 05, 2022)
19-1241908-C-T		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
19-1241909-G-C			Uncertain significance (May 21, 2022)
19-1241910-T-TGCCTATGCCGAGGCC			Uncertain significance (Jan 23, 2022)
19-1241913-C-T		ATP5F1D-related disorder	Likely benign (Jan 08, 2025)
19-1241919-C-T			Likely benign (Sep 01, 2022)
19-1241922-G-GGCC			Uncertain significance (May 31, 2023)
19-1241924-C-T			Uncertain significance (Aug 07, 2023)
19-1241930-C-A		Inborn genetic diseases	Uncertain significance (May 06, 2024)
19-1241933-C-T			Uncertain significance (Feb 24, 2024)
19-1241936-C-T			Uncertain significance (May 04, 2022)
19-1241945-C-T			Uncertain significance (Feb 24, 2024)

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