FMC1

gene
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Also known as HSPC268

Summary

FMC1 (formation of mitochondrial complex V assembly factor 1, HGNC:26946) is a protein-coding gene on chromosome 7q34, encoding Protein FMC1 homolog (Q96HJ9). Plays a role in the assembly/stability of the mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V).

Involved in mitochondrial proton-transporting ATP synthase complex assembly. Located in mitochondrion.

Source: NCBI Gene 154791 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 1 total — 1 likely-pathogenic
  • MANE Select transcript: NM_197964

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26946
Approved symbolFMC1
Nameformation of mitochondrial complex V assembly factor 1
Location7q34
Locus typegene with protein product
StatusApproved
AliasesHSPC268
Ensembl geneENSG00000164898
Ensembl biotypeprotein_coding
OMIM620766
Entrez154791

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000297534, ENST00000468383, ENST00000481123, ENST00000482181, ENST00000488886

RefSeq mRNA: 1 — MANE Select: NM_197964 NM_197964

CCDS: CCDS5853

Canonical transcript exons

ENST00000297534 — 2 exons

ExonStartEnd
ENSE00001636858139341337139341522
ENSE00001929279139345501139346328

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 98.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.4772 / max 100.5920, expressed in 1224 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
8144417.09561808
814401.2169619
814430.9811628
814390.2791144

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453398.42gold quality
right testisUBERON:000453498.15gold quality
testisUBERON:000047397.31gold quality
apex of heartUBERON:000209896.17gold quality
gastrocnemiusUBERON:000138894.88gold quality
skeletal muscle tissueUBERON:000113494.84gold quality
heart left ventricleUBERON:000208494.74gold quality
muscle of legUBERON:000138394.21gold quality
hindlimb stylopod muscleUBERON:000425293.74gold quality
right atrium auricular regionUBERON:000663193.44gold quality
heartUBERON:000094893.31gold quality
pituitary glandUBERON:000000792.96gold quality
adenohypophysisUBERON:000219692.95gold quality
right lobe of liverUBERON:000111492.79gold quality
substantia nigraUBERON:000203892.05gold quality
C1 segment of cervical spinal cordUBERON:000646991.94gold quality
putamenUBERON:000187491.66gold quality
lower esophagus muscularis layerUBERON:003583391.66gold quality
right adrenal glandUBERON:000123391.60gold quality
lower esophagusUBERON:001347391.59gold quality
right adrenal gland cortexUBERON:003582791.59gold quality
esophagogastric junction muscularis propriaUBERON:003584191.50gold quality
left lobe of thyroid glandUBERON:000112091.39gold quality
left adrenal gland cortexUBERON:003582591.25gold quality
left adrenal glandUBERON:000123491.23gold quality
adult mammalian kidneyUBERON:000008291.20gold quality
fundus of stomachUBERON:000116091.17gold quality
caudate nucleusUBERON:000187391.10gold quality
hypothalamusUBERON:000189891.10gold quality
amygdalaUBERON:000187691.03gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-10yes30.90
E-ANND-3yes16.95
E-MTAB-6524no88.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting FMC1, 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-3163100.0077.238605
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-428299.9975.366408
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-545-5P99.6670.182308
HSA-MIR-445299.5068.451493
HSA-MIR-608099.4369.43373
HSA-MIR-4797-5P99.3968.011354
HSA-MIR-427999.1966.702437
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-10399-5P99.1769.872610
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-628-3P99.0468.37814
HSA-MIR-1909-5P98.9464.01484
HSA-MIR-6761-5P98.7168.031504
HSA-MIR-619-5P98.5764.971988
HSA-MIR-451198.3267.971500

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosi:ch1073-314i13.4ENSDARG00000074266
mus_musculusFmc1ENSMUSG00000019689
rattus_norvegicusFmc1ENSRNOG00000005618
drosophila_melanogasterCG34117FBGN0083953
caenorhabditis_elegansWBGENE00016209

Protein

Protein identifiers

Protein FMC1 homologQ96HJ9 (reviewed: Q96HJ9)

Alternative names: ATP synthase assembly factor FMC1, mitochondrial, Formation of mitochondrial complex V assembly factor 1 homolog

All UniProt accessions (1): Q96HJ9

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the assembly/stability of the mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V).

Subunit / interactions. Interacts with ATPAF2.

Subcellular location. Mitochondrion.

Similarity. Belongs to the FMC1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96HJ9-11yes
Q96HJ9-22

RefSeq proteins (1): NP_932068* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR037667FMC1_homologueFamily

Pfam: PF13233

UniProt features (4 total): chain 1, region of interest 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96HJ9-F186.240.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 156 (showing top): GOBP_BEHAVIOR, TGCGCANK_UNKNOWN, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_LIPID_METABOLIC_PROCESS, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, GOBP_REGULATION_OF_CATABOLIC_PROCESS, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GOBP_LIPID_METABOLIC_PROCESS, WHN_B, GOBP_NEGATIVE_REGULATION_OF_LIPID_CATABOLIC_PROCESS, GOBP_DOPAMINERGIC_NEURON_DIFFERENTIATION

GO Biological Process (8): apoptotic mitochondrial changes (GO:0008637), response to toxic substance (GO:0009636), mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615), negative regulation of lipid catabolic process (GO:0050995), regulation of type B pancreatic cell proliferation (GO:0061469), motor behavior (GO:0061744), dopaminergic neuron differentiation (GO:0071542), mitochondrion organization (GO:0007005)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
apoptotic process1
mitochondrion organization1
response to chemical1
mitochondrion1
mitochondrial respiratory chain complex assembly1
proton-transporting ATP synthase complex assembly1
negative regulation of catabolic process1
lipid catabolic process1
negative regulation of lipid metabolic process1
regulation of lipid catabolic process1
type B pancreatic cell proliferation1
regulation of epithelial cell proliferation1
behavior1
neuron differentiation1
organelle organization1
binding1
cytoplasm1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

808 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FMC1LYRM9A8MSI8601
FMC1LYRM1O43325582
FMC1LYRM2Q9NU23580
FMC1ETFRF1Q6IPR1578
FMC1SDHAF1A6NFY7526
FMC1LYRM7Q5U5X0507
FMC1SDHAF3Q9NRP4449
FMC1CLEC2LP0C7M8446
FMC1LYRM4Q9HD34431
FMC1KLRG2A4D1S0419
FMC1UBN2Q6ZU65377
FMC1NDUFB9Q9Y6M9370
FMC1IFT56A0AVF1370
FMC1TMEM186Q96B77358
FMC1TRMT5Q32P41347
FMC1TIMM29Q9BSF4347

IntAct

43 interactions, top by confidence:

ABTypeScore
DLDPDHXpsi-mi:“MI:0914”(association)0.880
GRPEL2DBTpsi-mi:“MI:0914”(association)0.710
FECHPGRMC1psi-mi:“MI:0914”(association)0.700
KLHL22TMEM223psi-mi:“MI:0914”(association)0.640
COX4I1DBTpsi-mi:“MI:0914”(association)0.560
ATPAF2NDUFAB1psi-mi:“MI:0914”(association)0.530
OXLD1NUDT19psi-mi:“MI:0914”(association)0.350
SLC1A1TNFRSF10Bpsi-mi:“MI:0914”(association)0.350
FECHPGRMC1psi-mi:“MI:0914”(association)0.350
LIG3NDUFS6psi-mi:“MI:0914”(association)0.350
SSH3HSPA8psi-mi:“MI:0914”(association)0.350
ATP5F1APMPCBpsi-mi:“MI:0914”(association)0.350
FMC1NDUFAB1psi-mi:“MI:0914”(association)0.350
ATP5F1ANRDCpsi-mi:“MI:0914”(association)0.350
FMC1DNM1Lpsi-mi:“MI:0914”(association)0.350
FMC1POLRMTpsi-mi:“MI:0914”(association)0.350
RPS6KB2SRSF1psi-mi:“MI:0914”(association)0.350
S100A2PLEKHG3psi-mi:“MI:0914”(association)0.350
S100A6VWA8psi-mi:“MI:0914”(association)0.350
ABHD10VWA8psi-mi:“MI:0914”(association)0.350
CALML3MYO1Cpsi-mi:“MI:0914”(association)0.350
MTRF1MEIS1psi-mi:“MI:0914”(association)0.350
OXLD1PRORPpsi-mi:“MI:0914”(association)0.350
GIPGNPATpsi-mi:“MI:0914”(association)0.350

BioGRID (96): C7orf55 (Affinity Capture-MS), C7orf55 (Affinity Capture-MS), C7orf55 (Affinity Capture-MS), C7orf55 (Affinity Capture-MS), C7orf55 (Affinity Capture-MS), C7orf55-LUC7L2 (Affinity Capture-MS), ATPAF2 (Affinity Capture-MS), MRPL57 (Affinity Capture-MS), C7orf55-LUC7L2 (Affinity Capture-MS), NT5DC2 (Affinity Capture-MS), CYCS (Affinity Capture-MS), CLPX (Affinity Capture-MS), POLDIP2 (Affinity Capture-MS), SLC25A51 (Affinity Capture-MS), MRPL46 (Affinity Capture-MS)

ESM2 similar proteins: A3KNJ8, A3LNG8, A5DH70, A5DY61, A6S5Q0, A7EDS9, A7S1A4, A7S1H9, A7TI92, A9UL63, A9UMQ3, B5FXA0, B5FYC7, B5X5U9, B5XCZ6, B8JLQ0, B9WD12, C4R7H7, C4Y4R9, C5DEI4, C5DR94, C5MJD6, C7ZKY9, C9SBR9, D1Z4E1, G2TRM0, G2TRP8, O43325, O60068, P82116, Q04401, Q0UIG9, Q503U1, Q54F42, Q5A7N3, Q6BQH4, Q6CHK8, Q6CTI7, Q6CUY0, Q6FMR7

Diamond homologs: A7S1A4, A9UL63, Q3SZA2, Q4G012, Q8MNU8, Q96HJ9, Q9CR13

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Mitochondrial protein degradation618.0×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2503066NM_197964.5(FMC1):c.104A>G (p.Tyr35Cys)Likely pathogenic

SpliceAI

358 predictions. Top by Δscore:

VariantEffectΔscore
7:139341521:GG:Gdonor_gain1.0000
7:139341522:GG:Gdonor_gain1.0000
7:139341523:G:GAdonor_loss1.0000
7:139345620:GG:Gdonor_gain1.0000
7:139345621:GG:Gdonor_gain1.0000
7:139341523:G:GGdonor_gain0.9900
7:139345659:TCTC:Tdonor_gain0.9900
7:139341505:GCTT:Gdonor_gain0.9800
7:139345496:TCTA:Tacceptor_loss0.9800
7:139345498:TA:Tacceptor_loss0.9800
7:139345499:AGGT:Aacceptor_loss0.9800
7:139345606:G:GTdonor_gain0.9800
7:139341519:TCGG:Tdonor_gain0.9700
7:139345634:TGGAG:Tdonor_gain0.9700
7:139345635:GGAGG:Gdonor_gain0.9700
7:139341501:G:GTdonor_gain0.9600
7:139345617:C:Tdonor_gain0.9600
7:139345686:G:Tdonor_gain0.9600
7:139345761:A:AGdonor_gain0.9500
7:139341567:G:GTdonor_gain0.9400
7:139345498:TAGG:Tacceptor_gain0.9400
7:139345499:A:AGacceptor_gain0.9400
7:139345500:G:GGacceptor_gain0.9400
7:139345740:A:Tdonor_gain0.9400
7:139341563:G:GTdonor_gain0.9300
7:139341518:ATCGG:Adonor_gain0.9200
7:139341528:G:GTdonor_gain0.9200
7:139345497:CTAGG:Cacceptor_gain0.9200
7:139341564:G:Tdonor_gain0.9100
7:139345499:AGG:Aacceptor_gain0.9000

AlphaMissense

709 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:139345549:G:CA63P0.980
7:139345568:T:CL69P0.968
7:139345609:T:CF83L0.964
7:139345611:T:AF83L0.964
7:139345611:T:GF83L0.964
7:139345576:A:CS72R0.961
7:139345578:C:AS72R0.961
7:139345578:C:GS72R0.961
7:139341508:T:CF42L0.956
7:139341510:C:AF42L0.956
7:139341510:C:GF42L0.956
7:139345646:C:AA95D0.955
7:139345558:T:GY66D0.949
7:139345550:C:AA63D0.945
7:139345583:G:CR74P0.935
7:139341433:G:AE17K0.932
7:139345543:T:CF61L0.926
7:139345545:C:AF61L0.926
7:139345545:C:GF61L0.926
7:139345519:T:CC53R0.925
7:139345571:T:CL70P0.921
7:139345661:T:CL100P0.916
7:139345505:C:TT48I0.915
7:139345521:C:GC53W0.910
7:139345598:T:CL79P0.910
7:139341425:T:AL14H0.907
7:139341425:T:CL14P0.907
7:139345520:G:AC53Y0.907
7:139345577:G:TS72I0.903
7:139345645:G:CA95P0.902

dbSNP variants (sampled 300 via entrez): RS1000087403 (7:139339108 C>T), RS1000174566 (7:139339878 G>A), RS1000404486 (7:139345066 C>T), RS1000585773 (7:139342477 T>TG), RS1000614876 (7:139340084 T>C), RS1000737181 (7:139344804 G>A), RS1001216087 (7:139338730 A>G), RS1001705626 (7:139340270 G>A,T), RS1001777698 (7:139340457 C>A), RS1001826239 (7:139343467 T>C), RS1001918871 (7:139345606 G>C), RS1002427465 (7:139341923 C>A), RS1002782368 (7:139341089 C>G,T), RS1002947813 (7:139346819 T>C), RS1003390611 (7:139340755 C>G,T)

Disease associations

OMIM: gene MIM:620766 | disease phenotypes: MIM:276900

GenCC curated gene-disease

Mondo (1): Usher syndrome (MONDO:0019501)

Orphanet (1): Usher syndrome (Orphanet:886)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002875_124Diisocyanate-induced asthma1.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006995response to diisocyanate

MeSH disease descriptors (1)

DescriptorNameTree numbers
D052245Usher SyndromesC09.218.458.341.186.500.500; C09.218.458.341.887.886; C10.597.751.418.341.186.500.500; C10.597.751.418.341.887.886; C10.597.751.941.162.625.500; C11.768.585.658.500.813; C11.966.075.375.500; C16.131.077.299.500; C16.320.290.684.500; C23.888.592.763.393.341.887.886

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression5
trichostatin Aaffects cotreatment, decreases expression2
Cyclosporinedecreases expression2
FR900359affects phosphorylation1
beauvericinaffects cotreatment, increases expression1
bafilomycin A1decreases expression, decreases reaction1
CGP 52608affects binding, increases reaction1
enniatinsaffects cotreatment, increases expression1
entinostatdecreases expression1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
ICG 001increases expression1
dorsomorphinaffects cotreatment, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Temozolomidedecreases expression1
Carbonyl Cyanide m-Chlorophenyl Hydrazonedecreases expression, decreases reaction1
Cisplatindecreases expression1
Estradioldecreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Hydrogen Peroxideaffects expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Quercetindecreases expression1
Rotenoneincreases expression, increases reaction, decreases expression1
Tobacco Smoke Pollutionincreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Okadaic Aciddecreases expression1
Particulate Matteraffects cotreatment, decreases expression, increases abundance1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B5JRHAP1 C7orf55 (-) 2Cancer cell lineMale
CVCL_XM39HAP1 C7orf55 (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT07290530PHASE3NOT_YET_RECRUITING24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT02065011PHASE2ACTIVE_NOT_RECRUITINGA Study to Determine the Long-Term Safety, Tolerability and Biological Activity of SAR421869 in Patients With Usher Syndrome Type 1B
NCT01505062PHASE1/PHASE2TERMINATEDStudy of SAR421869 in Participants With Retinitis Pigmentosa Associated With Usher Syndrome Type 1B
NCT04355689PHASE1/PHASE2ACTIVE_NOT_RECRUITINGSafety and Efficacy of NPI-001 Tablets for RP Associated With Usher Syndrome
NCT06789445PHASE1/PHASE2RECRUITINGA Study to Investigate the Safety of OpCT-001 in Adults Who Have Primary Photoreceptor Disease (CLARICO)
NCT00004345Not specifiedTERMINATEDStudy of Dietary N-3 Fatty Acids in Patients With Retinitis Pigmentosa and Usher Syndrome
NCT00016471Not specifiedCOMPLETEDA Genetic Analysis of Usher Syndrome in Ashkenazi Jews
NCT00106743Not specifiedCOMPLETEDNatural History and Genetic Studies of Usher Syndrome
NCT01954953Not specifiedUNKNOWNClinical and Genetic Examination of Usher Syndrome Patients’ Cohort in Europe
NCT02435940Not specifiedRECRUITINGInherited Retinal Degenerative Disease Registry
NCT03319524Not specifiedCOMPLETEDClinical and Genetic Testing of Patients With Usher Syndrome
NCT03901391Not specifiedCOMPLETEDProspective Open Clinical and Genetic Study of Patients With Retinitis Pigmentosa
NCT03990727Not specifiedUNKNOWNPhenotype Correlates Genotype of Inherited Retina Dystrophies, Retinitis Pigmentosa, Con>Rod Dystrophies.
NCT04665726Not specifiedRECRUITINGNatural History Study of Usher Syndrome ( Light4Deaf )
NCT04906135Not specifiedCOMPLETEDAuditory Neural Function in Implanted Patients With Usher Syndrome
NCT05355415Not specifiedRECRUITINGAdaptive Optics Imaging of Outer Retinal Diseases
NCT07278843Not specifiedRECRUITINGNatural History of Photoreceptor Degeneration in USH1B: Clinical Parameters and Validation of Functional Vision Tests in MYO7A
NCT07548944Not specifiedRECRUITINGObservational Study to Investigate the Short-term Effects of Transcorneal Electrical Stimulation on Visual Performance
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Usher syndrome