ATP5MC3

gene
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Summary

ATP5MC3 (ATP synthase membrane subunit c locus 3, HGNC:843) is a protein-coding gene on chromosome 2q31.1, encoding ATP synthase F(0) complex subunit C3, mitochondrial (P48201). 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.

This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene is one of three genes that encode subunit c of the proton channel. Each of the three genes have distinct mitochondrial import sequences but encode the identical mature protein. Alternatively spliced transcript variants encoding different proteins have been identified.

Source: NCBI Gene 518 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): dystonia, early-onset, and/or spastic paraplegia (Strong, GenCC) — +1 more curated relationship
  • Clinical variants (ClinVar): 37 total — 2 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 9
  • MANE Select transcript: NM_001689

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:843
Approved symbolATP5MC3
NameATP synthase membrane subunit c locus 3
Location2q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000154518
Ensembl biotypeprotein_coding
OMIM602736
Entrez518

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 retained_intron

ENST00000284727, ENST00000392541, ENST00000409194, ENST00000472782, ENST00000497075, ENST00000877858, ENST00000877859, ENST00000877860, ENST00000877861, ENST00000937346, ENST00000937347, ENST00000937348, ENST00000937349, ENST00000937350, ENST00000941362

RefSeq mRNA: 3 — MANE Select: NM_001689 NM_001002258, NM_001190329, NM_001689

CCDS: CCDS2263

Canonical transcript exons

ENST00000284727 — 5 exons

ExonStartEnd
ENSE00001016410175176258175178402
ENSE00001016412175179057175179250
ENSE00001588911175181656175181710
ENSE00003574305175181355175181466
ENSE00003602002175180098175180178

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 99.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 188.0861 / max 1280.0117, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
31936186.19961826
319341.2035473
319350.4764184
319330.206671

Top tissues by expression

298 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
heart right ventricleUBERON:000208099.85gold quality
left ventricle myocardiumUBERON:000656699.79gold quality
cardiac ventricleUBERON:000208299.72gold quality
heart left ventricleUBERON:000208499.72gold quality
body of tongueUBERON:001187699.72gold quality
renal medullaUBERON:000036299.70gold quality
ponsUBERON:000098899.69gold quality
apex of heartUBERON:000209899.68gold quality
myocardiumUBERON:000234999.67gold quality
diaphragmUBERON:000110399.64gold quality
vena cavaUBERON:000408799.64gold quality
mucosa of transverse colonUBERON:000499199.64gold quality
cardiac atriumUBERON:000208199.62gold quality
cardiac muscle of right atriumUBERON:000337999.61gold quality
right atrium auricular regionUBERON:000663199.61gold quality
lateral nuclear group of thalamusUBERON:000273699.60gold quality
mucosa of sigmoid colonUBERON:000499399.60gold quality
colonic mucosaUBERON:000031799.56gold quality
jejunumUBERON:000211599.55gold quality
heartUBERON:000094899.54gold quality
penisUBERON:000098999.53gold quality
pharyngeal mucosaUBERON:000035599.52gold quality
jejunal mucosaUBERON:000039999.52gold quality
tongueUBERON:000172399.52gold quality
duodenumUBERON:000211499.52gold quality
vastus lateralisUBERON:000137999.46gold quality
superior surface of tongueUBERON:000737199.43gold quality
adult mammalian kidneyUBERON:000008299.41gold quality
quadriceps femorisUBERON:000137799.39gold quality
transverse colonUBERON:000115799.38gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 9.

ExperimentMarker?Max mean expression
E-HCAD-4yes136.19
E-MTAB-8410yes44.41
E-MTAB-9467yes30.32
E-CURD-122yes20.15
E-MTAB-10042yes16.65
E-HCAD-10yes12.15
E-CURD-112yes11.29
E-HCAD-25yes8.19
E-MTAB-7606no441.02
E-GEOD-125970no42.56
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

90 targeting ATP5MC3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-428299.9975.366408
HSA-MIR-477599.9875.006394
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-335-3P99.9373.364958
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-338-5P99.9272.342951
HSA-MIR-497-5P99.9271.832674
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-129799.9173.413162
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349

Literature-anchored findings (GeneRIF, showing 1)

  • ATP5G1, ATP5G2, and ATP5G3 of the ATP synthase are not involved in forming the permeability transition pore. (PMID:28289229)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioatp5mc3aENSDARG00000017775
mus_musculusAtp5mc3ENSMUSG00000018770
rattus_norvegicusAtp5mc3ENSRNOG00000001596

Paralogs (2): ATP5MC2 (ENSG00000135390), ATP5MC1 (ENSG00000159199)

Protein

Protein identifiers

ATP synthase F(0) complex subunit C3, mitochondrialP48201 (reviewed: P48201)

Alternative names: ATP synthase lipid-binding protein, ATP synthase membrane subunit c locus 3, ATP synthase proteolipid P3, ATP synthase proton-transporting mitochondrial F(0) complex subunit C3, ATPase protein 9, ATPase subunit c

All UniProt accessions (1): P48201

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c. Interacts with TMEM70 and TMEM242.

Subcellular location. Mitochondrion membrane.

Post-translational modifications. Trimethylated by ATPSCKMT at Lys-110. Methylation is required for proper incorporation of the C subunit into the ATP synthase complex and mitochondrial respiration.

Disease relevance. Dystonia, early-onset, and/or spastic paraplegia (DYTSPG) [MIM:619681] An autosomal dominant, highly penetrant movement disorder characterized by spastic paraplegia and/or dystonia to varying degrees in affected individuals. Cognition is not affected. There is high intra- and interfamilial variability in phenotype and age of onset. Some patients have onset of progressive focal or generalized dystonia in the first decade, whereas others develop progressive spastic paraplegia as adults. Some affected individuals have manifestations of both disorders. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. There are three genes which encode the mitochondrial ATP synthase proteolipid and they specify precursors with different import sequences but identical mature proteins. Is the major protein stored in the storage bodies of animals or humans affected with ceroid lipofuscinosis (Batten disease).

Similarity. Belongs to the ATPase C chain family.

RefSeq proteins (3): NP_001002258, NP_001177258, NP_001680* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000454ATP_synth_F0_csuFamily
IPR002379ATPase_proteolipid_c-like_domDomain
IPR020537ATP_synth_F0_csu_DDCD_BSBinding_site
IPR035921F/V-ATP_Csub_sfHomologous_superfamily
IPR038662ATP_synth_F0_csu_sfHomologous_superfamily

Pfam: PF00137

UniProt features (10 total): sequence variant 4, transmembrane region 2, transit peptide 1, chain 1, site 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P48201-F171.260.47

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 125 (reversibly protonated during proton transport)

Post-translational modifications (1): 110

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-163210Formation of ATP by chemiosmotic coupling
R-HSA-8949613Cristae formation
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-1592230Mitochondrial biogenesis
R-HSA-1852241Organelle biogenesis and maintenance

MSigDB gene sets: 336 (showing top): RNGTGGGC_UNKNOWN, MORF_DNMT1, RRAGTTGT_UNKNOWN, MORF_ESPL1, MODULE_151, GCM_NPM1, MORF_RRM1, MORF_HDAC1, MORF_UBE2N, HSIAO_HOUSEKEEPING_GENES, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, MORF_HDAC2, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS

GO Biological Process (3): proton motive force-driven ATP synthesis (GO:0015986), monoatomic ion transport (GO:0006811), proton transmembrane transport (GO:1902600)

GO Molecular Function (3): lipid binding (GO:0008289), proton transmembrane transporter activity (GO:0015078), protein binding (GO:0005515)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), proton-transporting two-sector ATPase complex, proton-transporting domain (GO:0033177), proton-transporting ATP synthase complex (GO:0045259), membrane (GO:0016020), mitochondrial membrane (GO:0031966)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Aerobic respiration and respiratory electron transport1
Mitochondrial biogenesis1
Metabolism1
Organelle biogenesis and maintenance1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
proton-transporting two-sector ATPase complex2
ATP biosynthetic process1
transport1
monoatomic cation transmembrane transport1
monoatomic cation transmembrane transporter activity1
proton transmembrane transport1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
membrane protein complex1
cation channel complex1
respiratory chain complex1
catalytic complex1
cellular anatomical structure1
mitochondrion1
mitochondrial envelope1
organelle membrane1

Protein interactions and networks

STRING

2550 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ATP5MC3UQCRFS1P47985920
ATP5MC3ATP5F1CP36542814
ATP5MC3ATP5PDO75947783
ATP5MC3CLCN3P51790765
ATP5MC3ATP5PBP24539750
ATP5MC3ATP5F1AP25705743
ATP5MC3ATP5F1EP56381726
ATP5MC3ATP5PFP18859720
ATP5MC3ATP5F1DP30049719
ATP5MC3ATP5F1BP06576716
ATP5MC3ACSF2Q96CM8710
ATP5MC3ATP5POP48047681
ATP5MC3RPL8P25120666
ATP5MC3EMC2Q15006622
ATP5MC3DMAC2LQ99766617

IntAct

20 interactions, top by confidence:

ABTypeScore
FPR2ARL6IP5psi-mi:“MI:0914”(association)0.640
ATP5MC3psi-mi:“MI:0915”(physical association)0.560
ATP5MC3ATP5F1Bpsi-mi:“MI:0914”(association)0.530
TMEM31PSMD11psi-mi:“MI:0914”(association)0.530
FAM241ANRP1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
AGPSpsi-mi:“MI:0915”(physical association)0.400
TK2psi-mi:“MI:0915”(physical association)0.400
MEP1BATP5MC3psi-mi:“MI:0915”(physical association)0.370
PROM1ATP5MC3psi-mi:“MI:0915”(physical association)0.370
DGCR2CCDC85Cpsi-mi:“MI:0914”(association)0.350
CD80RIMOC1psi-mi:“MI:0914”(association)0.350
HTR1EESYT2psi-mi:“MI:0914”(association)0.350
NIPAL2ATP5MC3psi-mi:“MI:0914”(association)0.350
SLC37A3PLXNB2psi-mi:“MI:0914”(association)0.350
ATP5MC3psi-mi:“MI:0915”(physical association)0.000
ABHD16AATP5MC3psi-mi:“MI:0915”(physical association)0.000

BioGRID (26): ATP5G3 (Affinity Capture-RNA), ATP5G3 (Affinity Capture-RNA), ATP5G3 (Two-hybrid), COL20A1 (Affinity Capture-MS), ATP5B (Affinity Capture-MS), GHDC (Affinity Capture-MS), ATP5D (Affinity Capture-MS), GOLGA4 (Affinity Capture-MS), ATP5G3 (Two-hybrid), ATP5G3 (PCA), ATP5G3 (Affinity Capture-MS), TMEM31 (Two-hybrid), ATP5G3 (Affinity Capture-RNA), ATP5B (Affinity Capture-MS), ATPIF1 (Affinity Capture-MS)

ESM2 similar proteins: A1XQS5, A6H666, A8XDX2, B0VYY5, B3DHU2, G5EDB8, O14046, P00842, P05496, P07926, P10175, P11432, P16000, P16221, P17605, P23968, P32876, P48201, P48772, P56383, P56384, Q01931, Q03672, Q06055, Q06056, Q06645, Q06646, Q0V9J0, Q0VCH8, Q2LCR3, Q2TA24, Q37315, Q3ZC75, Q53CG1, Q59550, Q5RAP9, Q5RFL2, Q5SWH9, Q71S46, Q7JX57

Diamond homologs: A1SHI6, A1XQS5, A3PN84, A4WNY7, A5CDC6, A6H4Q2, A8EX89, A8GLV9, A8GUJ2, A8XDX2, A9HDM8, A9RAH4, A9WGS9, B3CQT8, B8G6H1, B9LBM5, C0HK59, C3PM50, C4K0P2, O05331, O08310, P00840, P00842, P05496, P07926, P0C518, P0C519, P13547, P14571, P15014, P16000, P17254, P17605, P21537, P21905, P26855, P32876, P48201, P48880, P48881

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

37 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic1
Uncertain significance17
Likely benign3
Benign3

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
2500983NM_001689.5(ATP5MC3):c.319C>G (p.Pro107Ala)Pathogenic
2500984NM_001689.5(ATP5MC3):c.236G>T (p.Gly79Val)Pathogenic
976731NM_001689.5(ATP5MC3):c.318C>G (p.Asn106Lys)Likely pathogenic

SpliceAI

411 predictions. Top by Δscore:

VariantEffectΔscore
2:175179051:GATTA:Gdonor_loss1.0000
2:175179052:ATTAC:Adonor_loss1.0000
2:175179053:TTA:Tdonor_loss1.0000
2:175179054:TA:Tdonor_loss1.0000
2:175179055:A:ATdonor_loss1.0000
2:175179056:C:CTdonor_loss1.0000
2:175179246:GAGCC:Gacceptor_gain1.0000
2:175179248:GCC:Gacceptor_gain1.0000
2:175179249:CC:Cacceptor_gain1.0000
2:175179249:CCC:Cacceptor_gain1.0000
2:175179250:CC:Cacceptor_gain1.0000
2:175179251:C:CAacceptor_loss1.0000
2:175179251:C:CCacceptor_gain1.0000
2:175179252:T:Aacceptor_loss1.0000
2:175179259:C:CTacceptor_gain1.0000
2:175179260:A:Tacceptor_gain1.0000
2:175180094:TTAC:Tdonor_loss1.0000
2:175180095:TA:Tdonor_loss1.0000
2:175180096:ACCTC:Adonor_loss1.0000
2:175180097:C:CTdonor_loss1.0000
2:175180097:CCT:Cdonor_gain1.0000
2:175180114:G:Adonor_gain1.0000
2:175180174:CGGAT:Cacceptor_gain1.0000
2:175180179:C:Aacceptor_loss1.0000
2:175180179:C:CCacceptor_gain1.0000
2:175180180:T:Aacceptor_loss1.0000
2:175181350:CGCA:Cdonor_loss1.0000
2:175181353:A:ACdonor_gain1.0000
2:175181354:C:CCdonor_gain1.0000
2:175181354:C:CGdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000006288 (2:175178582 T>A,C), RS1000313646 (2:175177883 G>A), RS1000569638 (2:175183463 T>C), RS1000635497 (2:175177365 G>C), RS1000857866 (2:175176676 G>A,T), RS1001056534 (2:175182993 A>C), RS1001194482 (2:175183302 T>C), RS1001649088 (2:175177746 C>T), RS1002326307 (2:175181985 G>T), RS1002653812 (2:175176303 A>C), RS1002707612 (2:175175871 T>C), RS1003741271 (2:175181157 T>C), RS1003920824 (2:175182359 G>T), RS1003991203 (2:175181874 G>C), RS1004487018 (2:175176254 C>T)

Disease associations

OMIM: gene MIM:602736 | disease phenotypes: MIM:619681

GenCC curated gene-disease

DiseaseClassificationInheritance
dystonia, early-onset, and/or spastic paraplegiaStrongAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
mitochondrial diseaseLimitedAD

Mondo (1): dystonia, early-onset, and/or spastic paraplegia (MONDO:0859215)

Orphanet (0):

HPO phenotypes

9 total (9 of 9 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0001258Spastic paraplegia
HP:0001288Gait disturbance
HP:0001332Dystonia
HP:0001347Hyperreflexia
HP:0003581Adult onset
HP:0007340Lower limb muscle weakness
HP:0011463Childhood onset
HP:0012049Laryngeal dystonia

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs1982235ATP5MC30.000

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — F-type ATPase

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, increases expression5
bisphenol Aaffects expression, decreases expression, decreases methylation3
sodium arsenitedecreases expression, increases expression3
Air Pollutantsdecreases expression, increases abundance3
Cyclosporinedecreases expression3
Tunicamycindecreases expression2
Particulate Matterdecreases expression, increases abundance2
methylmercuric chloridedecreases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression, increases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
tris(chloroethyl)phosphatedecreases expression, increases abundance1
arsenic trichloridedecreases expression, increases abundance1
CD 437decreases expression1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, increases expression1
NSC 689534affects binding, decreases expression1
Acetaminophenaffects cotreatment, decreases expression1
Arsenicdecreases expression, increases abundance1
Catechindecreases expression, affects cotreatment1
Cocainedecreases expression1
Copperaffects binding, decreases expression1
Doxorubicinincreases expression1
Flame Retardantsdecreases expression, increases abundance1
Formaldehydedecreases expression1
Hydralazineincreases expression, affects cotreatment1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Methyl Methanesulfonatedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2SGAbcam HEK293T ATP5MC3 KOTransformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.