ATP5PF

ATP synthase peripheral stalk subunit F6, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 21:25716503-25735673

Previous symbols: [ "ATP5A", "ATP5", "ATPM", "ATP5J" ]

Links

ENSG00000154723 ∙ NCBI:522 ∙ OMIM:603152 ∙ HGNC:847 ∙ Uniprot:P18859 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5PF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5PF 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						0
missense			7			7
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in ATP5PF

This is a list of pathogenic ClinVar variants found in the ATP5PF region.

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

Position	Type	Phenotype	Significance	ClinVar
21-25724657-C-T		not specified	Uncertain significance (Jan 31, 2023)
21-25724675-G-C		not specified	Uncertain significance (Jul 19, 2022)
21-25725318-T-C		not specified	Uncertain significance (Dec 21, 2022)
21-25725345-G-C		not specified	Uncertain significance (Jun 22, 2023)
21-25729661-T-C		not specified	Uncertain significance (Apr 20, 2024)
21-25729695-T-C		not specified	Uncertain significance (Jan 23, 2023)
21-25729715-A-G		not specified	Uncertain significance (Nov 30, 2021)
21-25729731-G-A		not specified	Uncertain significance (Aug 16, 2021)
21-25729794-T-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5PF	protein_coding	protein_coding	ENST00000457143	4	19170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00613	0.753	125713	0	10	125723	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.428	52	61.4	0.846	0.00000315	762
Missense in Polyphen		11	12.243	0.89844		172
Synonymous	0.398	19	21.3	0.890	0.00000107	207
Loss of Function	0.857	4	6.33	0.632	3.43e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000321	0.0000321
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000187	0.000185
European (Non-Finnish)	0.0000448	0.0000440
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 synthesis 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(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements. Also involved in the restoration of oligomycin-sensitive ATPase activity to depleted F1-F0 complexes.
• Pathway: Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain;Oxidative phosphorylation;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;FOXA1 transcription factor network;Cristae formation;Mitochondrial biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;Validated nuclear estrogen receptor alpha network;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.95

Haploinsufficiency Scores

• pHI: 0.0339
• hipred: Y
• hipred_score: 0.507
• ghis: 0.424

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Atp5j

Gene ontology

• Biological process: ATP biosynthetic process;substantia nigra development;cristae formation;mitochondrial ATP synthesis coupled proton transport
• Cellular component: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o);mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex
• Molecular function: transporter activity;proton transmembrane transporter activity;ATPase activity;transmembrane transporter activity