ATP5MC1

ATP synthase membrane subunit c locus 1, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 17:48892765-48895871

Previous symbols: [ "ATP5G", "ATP5G1" ]

Links

ENSG00000159199 ∙ NCBI:516 ∙ OMIM:603192 ∙ HGNC:841 ∙ Uniprot:P05496 ∙ 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 ATP5MC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5MC1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ATP5MC1

This is a list of pathogenic ClinVar variants found in the ATP5MC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-48894373-T-A		not specified	Uncertain significance (Dec 16, 2022)
17-48894388-G-A		not specified	Uncertain significance (Jun 21, 2021)
17-48895192-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-48895195-G-C		not specified	Uncertain significance (Feb 28, 2024)
17-48895220-G-A		not specified	Uncertain significance (Apr 04, 2023)
17-48895232-C-T		not specified	Uncertain significance (Jun 27, 2022)
17-48895333-A-T		not specified	Uncertain significance (Aug 09, 2021)
17-48895738-T-C		not specified	Uncertain significance (Jan 04, 2024)
17-48895743-G-A		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5MC1	protein_coding	protein_coding	ENST00000393366	4	3107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.427	0.543	125730	0	4	125734	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	48	79.9	0.601	0.00000432	874
Missense in Polyphen		10	16.544	0.60445		247
Synonymous	0.153	30	31.1	0.965	0.00000168	290
Loss of Function	1.73	1	5.32	0.188	2.24e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	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(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element.
• 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;Metabolism of proteins;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;Mitochondrial protein import;Cristae formation;Mitochondrial biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.541
• hipred: Y
• hipred_score: 0.667
• ghis: 0.582

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atp5g1

Gene ontology

• Biological process: ATP biosynthetic process;ATP synthesis coupled proton transport;ATP hydrolysis coupled proton transport;cristae formation
• Cellular component: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o);mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex;integral component of membrane;proton-transporting ATP synthase complex, coupling factor F(o)
• Molecular function: transporter activity;protein binding;lipid binding;proton-transporting ATP synthase activity, rotational mechanism