ATP5MC2

ATP synthase membrane subunit c locus 2, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 12:53632725-53677408

Previous symbols: [ "ATP5G2" ]

Links

ENSG00000135390 ∙ NCBI:517 ∙ OMIM:603193 ∙ HGNC:842 ∙ Uniprot:Q06055 ∙ 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 ATP5MC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5MC2 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			2			2
Total	0	0	11	0	0

Variants in ATP5MC2

This is a list of pathogenic ClinVar variants found in the ATP5MC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53665364-T-G		not specified	Uncertain significance (May 22, 2023)
12-53665418-G-C		not specified	Uncertain significance (Apr 05, 2023)
12-53669190-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-53669254-C-T		not specified	Uncertain significance (Dec 13, 2022)
12-53669268-A-G		not specified	Uncertain significance (Sep 22, 2023)
12-53669333-G-C		not specified	Uncertain significance (May 16, 2024)
12-53669335-T-C		not specified	Uncertain significance (Jul 26, 2022)
12-53669917-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-53669920-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-53672604-C-T		not specified	Uncertain significance (Jun 10, 2022)
12-53672623-G-A		not specified	Uncertain significance (Dec 15, 2022)
12-53676093-G-C		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5MC2	protein_coding	protein_coding	ENST00000394349	5	44683

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000746	0.307	125724	0	21	125745	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	108	115	0.939	0.00000581	1254
Missense in Polyphen		23	26.658	0.86279		350
Synonymous	-0.757	55	48.3	1.14	0.00000267	452
Loss of Function	0.134	8	8.42	0.950	4.54e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000891	0.0000891
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000417	0.000416
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
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);Mitochondrial Electron Transport Chain;Electron Transport Chain;Oxidative phosphorylation;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;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: 0.0984

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.686
• hipred: N
• hipred_score: 0.461
• ghis: 0.530

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Atp5g2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype

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);mitochondrial outer 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