ECI1

gene
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Summary

ECI1 (enoyl-CoA delta isomerase 1, HGNC:2703) is a protein-coding gene on chromosome 16p13.3, encoding Enoyl-CoA delta isomerase 1, mitochondrial (P42126). Key enzyme of fatty acid beta-oxidation.

This gene encodes a member of the hydratase/isomerase superfamily. The protein encoded is a key mitochondrial enzyme involved in beta-oxidation of unsaturated fatty acids. It catalyzes the transformation of 3-cis and 3-trans-enoyl-CoA esters arising during the stepwise degradation of cis-, mono-, and polyunsaturated fatty acids to the 2-trans-enoyl-CoA intermediates. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 1632 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 98 total
  • Druggable target: yes
  • MANE Select transcript: NM_001919

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2703
Approved symbolECI1
Nameenoyl-CoA delta isomerase 1
Location16p13.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000167969
Ensembl biotypeprotein_coding
OMIM600305
Entrez1632

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 3 retained_intron

ENST00000301729, ENST00000561688, ENST00000562238, ENST00000563029, ENST00000563447, ENST00000566379, ENST00000570258, ENST00000857514, ENST00000857515, ENST00000857516, ENST00000957379, ENST00000957380, ENST00000957381

RefSeq mRNA: 2 — MANE Select: NM_001919 NM_001178029, NM_001919

CCDS: CCDS10464, CCDS58410

Canonical transcript exons

ENST00000301729 — 7 exons

ExonStartEnd
ENSE0000111881022430462243224
ENSE0000111881222394022240145
ENSE0000119748422515152251587
ENSE0000347362722513162251429
ENSE0000348237522433182243439
ENSE0000358556322468592246986
ENSE0000358846222444062244552

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 98.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 54.8052 / max 539.4646, expressed in 1818 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15591654.80521818

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209898.67gold quality
hindlimb stylopod muscleUBERON:000425297.93gold quality
right lobe of liverUBERON:000111497.82gold quality
gastrocnemiusUBERON:000138897.64gold quality
right atrium auricular regionUBERON:000663197.32gold quality
right lobe of thyroid glandUBERON:000111997.26gold quality
heart left ventricleUBERON:000208497.25gold quality
mucosa of transverse colonUBERON:000499197.06gold quality
cardiac ventricleUBERON:000208297.02gold quality
left lobe of thyroid glandUBERON:000112097.00gold quality
muscle of legUBERON:000138396.84gold quality
cardiac atriumUBERON:000208196.48gold quality
thyroid glandUBERON:000204696.18gold quality
metanephros cortexUBERON:001053396.10gold quality
muscle organUBERON:000163096.01gold quality
transverse colonUBERON:000115795.95gold quality
heartUBERON:000094895.90gold quality
lower esophagus muscularis layerUBERON:003583395.48gold quality
body of stomachUBERON:000116195.47gold quality
lower esophagusUBERON:001347395.47gold quality
olfactory segment of nasal mucosaUBERON:000538695.26gold quality
muscle layer of sigmoid colonUBERON:003580595.26gold quality
triceps brachiiUBERON:000150995.12gold quality
esophagogastric junction muscularis propriaUBERON:003584195.12gold quality
liverUBERON:000210795.09gold quality
right uterine tubeUBERON:000130294.89gold quality
adult mammalian kidneyUBERON:000008294.74gold quality
minor salivary glandUBERON:000183094.65gold quality
mucosa of stomachUBERON:000119994.63gold quality
saliva-secreting glandUBERON:000104494.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-10287yes46.72
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

  • determination of structure and mode of binding for fatty acyl group (PMID:15351645)
  • Hepatitis C virus growth and RNA replication in hepatoma cell lines stably expressing coenzyme A delta isomerase (DCI)-targeting short hairpin RNA (shRNA) were abrogated, indicating that DCI is required for productive infection. (PMID:21917952)
  • Fatty acid oxidation enzyme Delta3, Delta2-enoyl-CoA isomerase 1 (ECI1) drives aggressive tumor phenotype and predicts poor clinical outcome in prostate cancer patients. (PMID:35411033)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioeci1ENSDARG00000018002
mus_musculusEci1ENSMUSG00000024132
rattus_norvegicusEci1ENSRNOG00000008843
drosophila_melanogasterCG4598FBGN0032160
drosophila_melanogasterCG4594FBGN0032161
drosophila_melanogasterCG4592FBGN0032162

Paralogs (13): ECHDC1 (ENSG00000093144), ECH1 (ENSG00000104823), ECHDC2 (ENSG00000121310), ECHS1 (ENSG00000127884), CDY2B (ENSG00000129873), ECHDC3 (ENSG00000134463), AUH (ENSG00000148090), CDYL (ENSG00000153046), CDYL2 (ENSG00000166446), CDY1 (ENSG00000172288), CDY1B (ENSG00000172352), CDY2A (ENSG00000182415), HIBCH (ENSG00000198130)

Protein

Protein identifiers

Enoyl-CoA delta isomerase 1, mitochondrialP42126 (reviewed: P42126)

Alternative names: 3,2-trans-enoyl-CoA isomerase, Delta(3),Delta(2)-enoyl-CoA isomerase, Dodecenoyl-CoA isomerase

All UniProt accessions (4): P42126, A0A384NKJ3, H3BS70, Q96DC0

UniProt curated annotations — full annotation on UniProt →

Function. Key enzyme of fatty acid beta-oxidation. Able to isomerize both 3-cis (3Z) and 3-trans (3E) double bonds into the 2-trans (2E) form in a range of enoyl-CoA species, with a preference for (3Z)-enoyl-CoAs over (3E)-enoyl-CoAs. The catalytic efficiency of this enzyme is not affected by the fatty acyl chain length.

Subunit / interactions. Homotrimer.

Subcellular location. Mitochondrion matrix.

Tissue specificity. Expressed in liver (at protein level).

Pathway. Lipid metabolism; fatty acid beta-oxidation.

Similarity. Belongs to the enoyl-CoA hydratase/isomerase family.

Isoforms (2)

UniProt IDNamesCanonical?
P42126-11yes
P42126-22

RefSeq proteins (2): NP_001171500, NP_001910* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001753Enoyl-CoA_hydra/isoDomain
IPR018376Enoyl-CoA_hyd/isom_CSConserved_site
IPR029045ClpP/crotonase-like_dom_sfHomologous_superfamily

Pfam: PF00378

Enzyme classification (BRENDA):

  • EC 5.3.3.8 — DELTA3-DELTA2-enoyl-CoA isomerase (BRENDA: 14 organisms, 65 substrates, 8 inhibitors, 70 Km, 69 kcat entries)

Substrate kinetics (BRENDA)

19 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
3-TRANS-HEXENOYL-COA0.03–1.615
TRANS-3-HEXENOYL-COA0.03–0.127
3-CIS-HEXENOYL-COA0.031–1.26
3-CIS-TETRADECENOYL-COA0.006–0.0895
2-TRANS,5-CIS-OCTADIENOYL-COA0.0044–0.173
2-TRANS,5-CIS-TETRADECADIENOYL-COA0.0096–0.0293
3-CIS-OCTENOYL-COA0.032–0.153
3-DECYNOYL-N-ACETYLCYSTEAMINE0.24–0.813
3-DODECYNOYL-N-ACETYLCYSTEAMINE0.28–0.973
3-HEXYNOYL-N-ACETYLCYSTEAMINE2.1–7.23
3-OCTYNOYL-N-ACETYLCYSTEAMINE0.68–1.63
3-TRANS-OCTENOYL-COA0.028–0.193
3-TRANS-TETRADECENOYL-COA0.029–0.0483
TRANS-2-HEXENOYL-COA0.0006–0.313
3-HEXENOYL-COA0.04–0.152

Catalyzed reactions (Rhea), 7 shown:

  • (3Z)-dodecenoyl-CoA = (2E)-dodecenoyl-CoA (RHEA:23716)
  • (2E)-tetradecenoyl-CoA = (3Z)-tetradecenoyl-CoA (RHEA:29847)
  • a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA (RHEA:45228)
  • (3Z)-hexenoyl-CoA = (2E)-hexenoyl-CoA (RHEA:45748)
  • a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA (RHEA:45900)
  • (3Z)-octenoyl-CoA = (2E)-octenoyl-CoA (RHEA:46044)
  • (3Z)-decenoyl-CoA = (2E)-decenoyl-CoA (RHEA:77195)

UniProt features (54 total): sequence conflict 15, helix 14, strand 8, modified residue 7, binding site 3, turn 2, transit peptide 1, chain 1, splice variant 1, mutagenesis site 1, site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1SG4X-RAY DIFFRACTION1.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P42126-F190.430.86

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): 178 (important for catalytic activity)

Ligand- & substrate-binding residues (3): 106–110; 153; 177

Post-translational modifications (7): 283, 283, 288, 61, 61, 84, 89

Mutagenesis-validated functional residues (1):

PositionPhenotype
178loss of activity.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-77288mitochondrial fatty acid beta-oxidation of unsaturated fatty acids
R-HSA-9837999Mitochondrial protein degradation

MSigDB gene sets: 215 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_LIPID_MODIFICATION, GOBP_FATTY_ACID_CATABOLIC_PROCESS, MODULE_151, GOLDRATH_IMMUNE_MEMORY, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, HUMMERICH_SKIN_CANCER_PROGRESSION_DN, YGACNNYACAR_UNKNOWN, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS

GO Biological Process (3): fatty acid beta-oxidation (GO:0006635), lipid metabolic process (GO:0006629), fatty acid metabolic process (GO:0006631)

GO Molecular Function (4): delta(3)-delta(2)-enoyl-CoA isomerase activity (GO:0004165), intramolecular oxidoreductase activity, transposing C=C bonds (GO:0016863), catalytic activity (GO:0003824), isomerase activity (GO:0016853)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Mitochondrial Fatty Acid Beta-Oxidation1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
fatty acid catabolic process1
fatty acid ligase activity1
fatty acid oxidation1
primary metabolic process1
lipid metabolic process1
monocarboxylic acid metabolic process1
intramolecular oxidoreductase activity, transposing C=C bonds1
intramolecular oxidoreductase activity1
molecular_function1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1

Protein interactions and networks

STRING

2524 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ECI1ECI2O75521985
ECI1DECR1Q16698621
ECI1ACAA2P42765599
ECI1ACADSP16219556
ECI1HADHBP55084545
ECI1ETFDHQ16134544
ECI1HSD17B4P51659543
ECI1ACADLP28330539
ECI1ACADMP11310534
ECI1CPT2P23786516
ECI1ACADVLP49748507
ECI1DECR2Q9NUI1496
ECI1EHHADHQ08426480
ECI1ACOX3O15254463
ECI1ACADSBP45954456

IntAct

14 interactions, top by confidence:

ABTypeScore
LMTK3GPIpsi-mi:“MI:0914”(association)0.420
ECI1POT1psi-mi:“MI:0915”(physical association)0.370
MAPKAP1ECI1psi-mi:“MI:0915”(physical association)0.370
FASTKD3VWA8psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
RAB9ALANCL1psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
FBXL19S100A9psi-mi:“MI:0914”(association)0.350
DENND11psi-mi:“MI:0914”(association)0.350
VCPFAM171A2psi-mi:“MI:0914”(association)0.350
MRPL58psi-mi:“MI:0914”(association)0.350
HSPD1VWA8psi-mi:“MI:2364”(proximity)0.270

BioGRID (77): ECI1 (Co-fractionation), ECI1 (Co-fractionation), ECI1 (Co-fractionation), HIBCH (Co-fractionation), ECI1 (Affinity Capture-RNA), ECI1 (Affinity Capture-MS), ECI1 (Proximity Label-MS), ECI1 (Affinity Capture-MS), ECI1 (Proximity Label-MS), ECI1 (Co-fractionation), HMGCS1 (Co-fractionation), CHID1 (Co-fractionation), ACP6 (Co-fractionation), NFU1 (Co-fractionation), ECI1 (Co-fractionation)

ESM2 similar proteins: A6QP05, A9JS71, F1NB38, F1R6N4, O35459, P11172, P13439, P17256, P23965, P31754, P42125, P42126, Q03426, Q0V8R7, Q13011, Q28C91, Q28DB5, Q2HJD5, Q3MIE0, Q3URE1, Q4G176, Q58DN7, Q5E9H9, Q5E9T8, Q5HZQ8, Q5R4W0, Q5R514, Q5R824, Q5REX5, Q5RFG0, Q62651, Q62904, Q64323, Q6AYG5, Q6GLK6, Q6GM82, Q6NYL5, Q6PE15, Q7T0X7, Q8BGT5

Diamond homologs: A0KV76, A1ADI8, A1S7L6, A3CYJ4, A3QFP3, A4WCW6, A4XSM8, A5WH99, A6TC19, A7N1D2, A7ZPF8, A8A2L0, A8ADP2, A8G8D1, A9N453, B0KH74, B1IXA5, B1LME7, B1X9L4, B2TWV4, B4SZR0, B4TCA8, B4TQC2, B5BBA1, B5EZR9, B5FPN1, B5R3R9, B5RCL3, B5XVW2, B5YXY4, B6I6Q4, B7LBJ5, B7LLD0, B7M6M2, B7MGV7, B7MY16, B7N5V2, B7NP24, B7UFZ8, B7VGL4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance73
Likely benign5
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1207 predictions. Top by Δscore:

VariantEffectΔscore
16:2240142:TGGT:Tacceptor_gain1.0000
16:2240145:TC:Tacceptor_loss1.0000
16:2240146:C:CCacceptor_gain1.0000
16:2240147:T:Cacceptor_loss1.0000
16:2243220:TCAAC:Tacceptor_gain1.0000
16:2243221:CAAC:Cacceptor_gain1.0000
16:2243221:CAACC:Cacceptor_gain1.0000
16:2243222:AAC:Aacceptor_gain1.0000
16:2243223:AC:Aacceptor_gain1.0000
16:2243223:ACC:Aacceptor_loss1.0000
16:2243224:CC:Cacceptor_gain1.0000
16:2243224:CCT:Cacceptor_loss1.0000
16:2243225:C:CCacceptor_gain1.0000
16:2243225:CTGGA:Cacceptor_loss1.0000
16:2243311:GCCTT:Gdonor_loss1.0000
16:2243312:CCTTA:Cdonor_loss1.0000
16:2243313:CTTA:Cdonor_loss1.0000
16:2243314:TTA:Tdonor_loss1.0000
16:2243315:TA:Tdonor_loss1.0000
16:2243436:CTCC:Cacceptor_gain1.0000
16:2243437:TCC:Tacceptor_gain1.0000
16:2243438:CC:Cacceptor_gain1.0000
16:2243438:CCC:Cacceptor_gain1.0000
16:2243439:CC:Cacceptor_gain1.0000
16:2243439:CCTG:Cacceptor_loss1.0000
16:2243440:C:CCacceptor_gain1.0000
16:2243440:CTGCA:Cacceptor_loss1.0000
16:2243441:T:Gacceptor_loss1.0000
16:2244404:A:ACdonor_gain1.0000
16:2244405:C:CCdonor_gain1.0000

AlphaMissense

1928 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:2240123:C:AK255N0.995
16:2240123:C:GK255N0.995
16:2240136:C:GR251P0.994
16:2243319:A:GW188R0.993
16:2243319:A:TW188R0.993
16:2240112:C:GR259P0.992
16:2243396:T:AD162V0.991
16:2243431:G:CC150W0.990
16:2246949:G:CN68K0.990
16:2246949:G:TN68K0.990
16:2243390:C:GR164P0.989
16:2243438:C:TG148E0.989
16:2244535:G:CF104L0.989
16:2244535:G:TF104L0.989
16:2244537:A:GF104L0.989
16:2243357:C:TG175E0.988
16:2243117:T:AD224V0.987
16:2243163:C:AG209W0.985
16:2243396:T:GD162A0.985
16:2244453:A:GW132R0.985
16:2244453:A:TW132R0.985
16:2243398:A:CC161W0.984
16:2243397:C:AD162Y0.982
16:2244419:A:TV143D0.982
16:2243391:G:TR164S0.981
16:2243433:A:GC150R0.981
16:2243120:A:TV223E0.980
16:2243418:A:GC155R0.979
16:2243438:C:AG148V0.979
16:2246875:C:TG93D0.978

dbSNP variants (sampled 300 via entrez): RS1000088254 (16:2250045 T>G), RS1000303889 (16:2241410 C>G), RS1000326445 (16:2252061 TG>T), RS1000359220 (16:2250555 G>A,C,T), RS1000411169 (16:2245406 G>A), RS1000710985 (16:2250328 T>C), RS1000753426 (16:2239156 C>T), RS1000997342 (16:2243347 C>A,G), RS1001179360 (16:2242147 C>A,G,T), RS1001195667 (16:2249536 G>C,T), RS1001233060 (16:2244925 T>C), RS1001356470 (16:2240761 A>G), RS1001358369 (16:2242791 T>A,C), RS1001482484 (16:2250903 C>T), RS1001661277 (16:2245077 G>A,C)

Disease associations

OMIM: gene MIM:600305 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST007490_26Anthropometric traits (multi-trait analysis)1.000000e-11
GCST90011900_122Serum alkaline phosphatase levels2.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004324body weights and measures
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066903 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.30Kd5015nMCHEMBL3752910
5.30ED505015nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148281: Binding affinity to human ECI1 incubated for 45 mins by Kinobead based pull down assaykd5.0151uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases methylation4
sodium arsenitedecreases expression, increases abundance, increases expression2
Arsenicaffects methylation, decreases expression, increases abundance2
Tobacco Smoke Pollutionaffects expression, increases expression2
Tretinoinincreases expression2
aristolochic acid Idecreases expression, increases expression1
bisphenol Fincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
methylselenic aciddecreases expression1
beta-lapachonedecreases expression1
zinc chromateincreases abundance, decreases expression1
ochratoxin Adecreases expression1
tamibaroteneaffects expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
bisphenol Bincreases expression1
pyrachlostrobindecreases expression1
jinfukangincreases expression1
LDN 193189affects cotreatment, increases expression1
picoxystrobindecreases 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
Temozolomideincreases expression1
Sunitinibincreases expression1
Arsenic Trioxidedecreases response to substance1
Air Pollutantsdecreases expression, increases abundance1
Antimycin Adecreases expression1
Atrazinedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651323BindingBinding affinity to human ECI1 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.