ATP5F1C

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

Basic information

Region (hg38): 10:7788146-7807815

Previous symbols: [ "ATP5CL1", "ATP5C", "ATP5C1" ]

Links

ENSG00000165629 ∙ NCBI:509 ∙ OMIM:108729 ∙ HGNC:833 ∙ Uniprot:P36542 ∙ 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 ATP5F1C gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5F1C 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in ATP5F1C

This is a list of pathogenic ClinVar variants found in the ATP5F1C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-7788242-C-T		not specified	Uncertain significance (Sep 20, 2023)
10-7788251-T-C		not specified	Uncertain significance (Jun 23, 2021)
10-7797101-A-G		not specified	Uncertain significance (May 24, 2023)
10-7797110-C-T		not specified	Uncertain significance (Jul 25, 2023)
10-7797131-C-T		not specified	Uncertain significance (Aug 14, 2023)
10-7799020-C-T		not specified	Uncertain significance (Jun 24, 2022)
10-7799114-C-A		not specified	Uncertain significance (Dec 15, 2023)
10-7802277-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-7802348-A-G		not specified	Uncertain significance (Jan 23, 2024)
10-7802423-C-T		not specified	Uncertain significance (Jul 05, 2023)
10-7802793-C-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5F1C	protein_coding	protein_coding	ENST00000356708	9	19687

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000792	0.985	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.800	134	163	0.824	0.00000809	1950
Missense in Polyphen		31	49.38	0.62778		684
Synonymous	1.41	45	58.8	0.766	0.00000312	569
Loss of Function	2.15	8	17.8	0.450	0.00000103	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.0000546	0.0000544
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(1) domain and the central stalk which is part of the complex rotary element. The gamma subunit protrudes into the catalytic domain formed of alpha(3)beta(3). 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. {ECO:0000250|UniProtKB:P05631}.
• 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;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;EGFR1;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: 0.570

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.312
• hipred: Y
• hipred_score: 0.783
• ghis: 0.635

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Atp5c1

Gene ontology

• Biological process: oxidative phosphorylation;ATP biosynthetic process;ATP synthesis coupled proton transport;cristae formation;mitochondrial ATP synthesis coupled proton transport;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;membrane;myelin sheath
• Molecular function: RNA binding;ATPase activity;transmembrane transporter activity;proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATPase activity, rotational mechanism