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ECHDC3

gene
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Also known as FLJ20909

Summary

ECHDC3 (enoyl-CoA hydratase domain containing 3, HGNC:23489) is a protein-coding gene on chromosome 10p14, encoding Enoyl-CoA hydratase domain-containing protein 3, mitochondrial (Q96DC8). May play a role in fatty acid biosynthesis and insulin sensitivity.

Predicted to enable enoyl-CoA hydratase activity. Involved in positive regulation of cellular response to insulin stimulus. Located in mitochondrion.

Source: NCBI Gene 79746 — RefSeq curated summary.

At a glance

  • GWAS associations: 13
  • Clinical variants (ClinVar): 43 total
  • MANE Select transcript: NM_024693

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23489
Approved symbolECHDC3
Nameenoyl-CoA hydratase domain containing 3
Location10p14
Locus typegene with protein product
StatusApproved
AliasesFLJ20909
Ensembl geneENSG00000134463
Ensembl biotypeprotein_coding
OMIM620756
Entrez79746

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000379215, ENST00000420401, ENST00000422887, ENST00000495787, ENST00000496136, ENST00000883992, ENST00000883993, ENST00000883994, ENST00000957896

RefSeq mRNA: 1 — MANE Select: NM_024693 NM_024693

CCDS: CCDS7084

Canonical transcript exons

ENST00000379215 — 5 exons

ExonStartEnd
ENSE000034655241176322411764070
ENSE000035033521174734911747470
ENSE000035927761175540811755608
ENSE000036250751174949511749592
ENSE000036784871174238211742746

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 97.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.6647 / max 183.7178, expressed in 1303 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1038956.02251289
1038970.2686112
1038960.204490
1038980.169275

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111497.21gold quality
gastrocnemiusUBERON:000138895.42gold quality
adult mammalian kidneyUBERON:000008295.24gold quality
liverUBERON:000210795.05gold quality
nephron tubuleUBERON:000123195.00gold quality
tibialis anteriorUBERON:000138594.67gold quality
heart left ventricleUBERON:000208494.56gold quality
cardiac ventricleUBERON:000208294.28gold quality
apex of heartUBERON:000209894.09gold quality
muscle of legUBERON:000138393.44gold quality
adipose tissueUBERON:000101392.68gold quality
kidney epitheliumUBERON:000481992.59gold quality
adipose tissue of abdominal regionUBERON:000780892.32gold quality
omental fat padUBERON:001041492.04gold quality
peritoneumUBERON:000235891.97gold quality
hindlimb stylopod muscleUBERON:000425291.94gold quality
right atrium auricular regionUBERON:000663191.94gold quality
muscle organUBERON:000163091.88gold quality
heartUBERON:000094891.66gold quality
subcutaneous adipose tissueUBERON:000219091.53gold quality
cardiac atriumUBERON:000208191.48gold quality
adult organismUBERON:000702391.45gold quality
kidneyUBERON:000211391.36gold quality
connective tissueUBERON:000238491.25gold quality
right lungUBERON:000216790.97gold quality
right adrenal glandUBERON:000123390.82gold quality
right adrenal gland cortexUBERON:003582790.23gold quality
lower esophagus mucosaUBERON:003583490.09gold quality
cortex of kidneyUBERON:000122589.99gold quality
metanephric glomerulusUBERON:000473689.87gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting ECHDC3, 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-34A-5P99.9971.211784
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-311999.9271.342390
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-425-5P99.5967.67900
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-330-3P99.4169.952521
HSA-MIR-391199.3866.951087
HSA-MIR-578799.2267.862628
HSA-MIR-4699-5P98.9967.501210
HSA-MIR-6728-3P98.6367.631534
HSA-MIR-4720-3P98.5068.88988
HSA-MIR-224-5P98.3370.121256
HSA-MIR-4640-5P97.4266.331543
HSA-MIR-4726-5P97.2465.671299
HSA-MIR-4474-3P96.9765.87870
HSA-MIR-3184-3P96.9666.91845
HSA-MIR-4764-3P96.8167.94580
HSA-MIR-208A-3P95.8766.51397
HSA-MIR-208B-3P95.8766.56396

Literature-anchored findings (GeneRIF, showing 4)

  • Increased levels of monounsaturated fatty acids, especially oleic acid, and ECHDC3 upregulation in patients with coronary artery lesion suggests that these are independent factors associated with the initial progression of cardiovascular disease. (PMID:27586541)
  • Genome-wide significant (GWS) associations in single-nucleotide polymorphism (SNP)-based tests (P < 5 x 10(-8)) were identified for SNPs in PFDN1/HBEGF, USP6NL/ECHDC3, and BZRAP1-AS1. (PMID:28183528)
  • Genetically (cis-) regulated expression of adipose tissue enoyl-CoA hydratase domain-containing 3 (ECHDC3) and genetic silencing studies in a human adipocyte model suggest that ECHDC3 may play an important role in determining insulin sensitivity. (PMID:31010960)
  • ECHDC3 Variant Regulates the Right Hippocampal Microstructural Integrity and Verbal Memory in Type 2 Diabetes Mellitus. (PMID:38070593)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusEchdc3ENSMUSG00000039063
rattus_norvegicusEchdc3ENSRNOG00000048114
drosophila_melanogasterCG6984FBGN0034191
caenorhabditis_elegansWBGENE00001151

Paralogs (13): ECHDC1 (ENSG00000093144), ECH1 (ENSG00000104823), ECHDC2 (ENSG00000121310), ECHS1 (ENSG00000127884), CDY2B (ENSG00000129873), AUH (ENSG00000148090), CDYL (ENSG00000153046), CDYL2 (ENSG00000166446), ECI1 (ENSG00000167969), CDY1 (ENSG00000172288), CDY1B (ENSG00000172352), CDY2A (ENSG00000182415), HIBCH (ENSG00000198130)

Protein

Protein identifiers

Enoyl-CoA hydratase domain-containing protein 3, mitochondrial — Q96DC8 (reviewed: Q96DC8)

All UniProt accessions (3): Q96DC8, Q5W0J6, Q5W0J8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in fatty acid biosynthesis and insulin sensitivity.

Subcellular location. Mitochondrion.

Tissue specificity. Expressed in adipocytes. Expressed in blood cells, with higher expression in patients with low coronary lesions.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q96DC8-11yes
Q96DC8-22

RefSeq proteins (1): NP_078969* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001753Enoyl-CoA_hydra/isoDomain
IPR014748Enoyl-CoA_hydra_CHomologous_superfamily
IPR029045ClpP/crotonase-like_dom_sfHomologous_superfamily
IPR052377Mitochondrial_ECH-domainFamily

Pfam: PF00378

UniProt features (32 total): helix 14, strand 8, sequence variant 3, sequence conflict 2, transit peptide 1, chain 1, turn 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2VX2X-RAY DIFFRACTION2.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DC8-F190.440.84

Functional residue map

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

Post-translational modifications (1): 110

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_CELLULAR_RESPONSE_TO_INSULIN_STIMULUS, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, GOBP_RESPONSE_TO_INSULIN, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_POSITIVE_REGULATION_OF_CELLULAR_RESPONSE_TO_INSULIN_STIMULUS, GOBP_CELLULAR_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_HORMONE, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOMF_HYDRO_LYASE_ACTIVITY

GO Biological Process (3): fatty acid metabolic process (GO:0006631), positive regulation of cellular response to insulin stimulus (GO:1900078), lipid metabolic process (GO:0006629)

GO Molecular Function (2): enoyl-CoA hydratase activity (GO:0004300), hydro-lyase activity (GO:0016836)

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

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid metabolic process1
monocarboxylic acid metabolic process1
cellular response to insulin stimulus1
positive regulation of cellular process1
positive regulation of response to stimulus1
regulation of cellular response to insulin stimulus1
primary metabolic process1
hydro-lyase activity1
carbon-oxygen lyase activity1
cytoplasm1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ECHDC3USP6NLQ92738569
ECHDC3SCIMPQ6UWF3541
ECHDC3HS3ST1O14792505
ECHDC3CASS4Q9NQ75497
ECHDC3PROSER2Q86WR7496
ECHDC3ABCA7Q8IZY2478
ECHDC3NME8Q8N427475
ECHDC3ABI3Q9P2A4442
ECHDC3ZCWPW1Q9H0M4436
ECHDC3TSPOAP1O95153419
ECHDC3SLC24A4Q8NFF2418
ECHDC3MS4A6AQ9H2W1417
ECHDC3SORL1Q92673406
ECHDC3PFDN1O60925398
ECHDC3INPP5DQ92835398

IntAct

9 interactions, top by confidence:

ABTypeScore
UQCRFS1NDUFAB1psi-mi:“MI:0914”(association)0.530
NUDT19psi-mi:“MI:0914”(association)0.350
RASL10BVWA8psi-mi:“MI:0914”(association)0.350
AK4VWA8psi-mi:“MI:0914”(association)0.350
GPR45VWA8psi-mi:“MI:0914”(association)0.350
NIPSNAP3ANUDT19psi-mi:“MI:0914”(association)0.350
LDHAL6BCPS1psi-mi:“MI:0914”(association)0.350
purCDECHDC3psi-mi:“MI:0915”(physical association)0.000

BioGRID (12): ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Affinity Capture-MS), ECHDC3 (Co-fractionation), ECHDC3 (Co-fractionation), ECHDC3 (Co-fractionation), ECHDC3 (Co-fractionation)

ESM2 similar proteins: A0PJR5, A2C0Z2, A4SGK0, A5VSZ7, A6UCL8, A6WXC3, A7HTW0, A9BEF8, A9HL57, A9JS71, A9M9B7, B0CJD4, B2S8T2, B3PPF4, B5ZSI8, B9JBU0, C0RFS3, C3MHX3, F1R6N4, O75521, O87873, P52045, Q11DU2, Q1MB43, Q21LR0, Q28C91, Q2K3L0, Q2T4M6, Q2VZG7, Q3MIE0, Q46GP3, Q50130, Q57AM5, Q5HZQ8, Q5M8W9, Q5NPY2, Q5XIC0, Q6NL24, Q6NY77, Q78JN3

Diamond homologs: A0A481WNM8, A0PJR5, A0R4Q3, A8ALR7, A9JS71, A9MR28, A9MYJ5, B1IRE0, B1LFW9, B4EY26, B4T6J5, B4TIG9, B4TWR3, B5BL54, B5F749, B5FHG4, B5R1Q9, B5RGA4, B7NP24, C0Q4L2, C5NN19, G4V4T7, P31551, P52045, P59395, P76082, P9WNN6, P9WNN7, Q0AVM1, Q0TLV3, Q3MIE0, Q50130, Q57TJ1, Q5PIL1, Q5XIC0, Q5ZJ60, Q7U004, Q8BH95, Q8FLA6, Q8GB17

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance33
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1152 predictions. Top by Δscore:

VariantEffectΔscore
10:11747343:TCACA:Tacceptor_loss1.0000
10:11747344:CACA:Cacceptor_loss1.0000
10:11747346:CAGGA:Cacceptor_loss1.0000
10:11747347:A:Cacceptor_loss1.0000
10:11747348:GGAAC:Gacceptor_gain1.0000
10:11747468:CGG:Cdonor_gain1.0000
10:11747468:CGGG:Cdonor_loss1.0000
10:11747469:GG:Gdonor_gain1.0000
10:11747469:GGG:Gdonor_gain1.0000
10:11747470:GG:Gdonor_gain1.0000
10:11747470:GGTA:Gdonor_loss1.0000
10:11747471:G:GAdonor_loss1.0000
10:11747471:G:GGdonor_gain1.0000
10:11747472:T:Adonor_loss1.0000
10:11749477:A:AGacceptor_gain1.0000
10:11749477:AATT:Aacceptor_gain1.0000
10:11749477:AATTG:Aacceptor_gain1.0000
10:11749478:A:Gacceptor_gain1.0000
10:11749478:ATT:Aacceptor_gain1.0000
10:11749478:ATTG:Aacceptor_gain1.0000
10:11749480:T:TAacceptor_gain1.0000
10:11749481:G:Aacceptor_gain1.0000
10:11763218:CCGTA:Cacceptor_loss1.0000
10:11763223:G:GAacceptor_loss1.0000
10:11747333:AAAAT:Aacceptor_gain0.9900
10:11747347:A:AGacceptor_gain0.9900
10:11747347:AG:Aacceptor_gain0.9900
10:11747348:G:GTacceptor_gain0.9900
10:11747348:GG:Gacceptor_gain0.9900
10:11747348:GGA:Gacceptor_gain0.9900

AlphaMissense

1964 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:11749509:T:CF103L0.991
10:11749511:T:AF103L0.991
10:11749511:T:GF103L0.991
10:11755448:C:AA144D0.988
10:11755490:T:AV158D0.988
10:11763500:T:CF290L0.987
10:11763502:C:AF290L0.987
10:11763502:C:GF290L0.987
10:11763388:A:CK252N0.985
10:11763388:A:TK252N0.985
10:11755466:C:AA150D0.984
10:11755514:C:AA166E0.983
10:11755532:T:CF172S0.983
10:11755561:T:CF182L0.983
10:11755563:C:AF182L0.983
10:11755563:C:GF182L0.983
10:11755498:T:CC161R0.981
10:11755502:A:TD162V0.981
10:11755566:T:GC183W0.981
10:11763362:A:CS244R0.980
10:11763364:C:AS244R0.980
10:11763364:C:GS244R0.980
10:11749510:T:CF103S0.979
10:11763384:G:AG251D0.979
10:11755445:T:AI143N0.978
10:11755480:T:CC155R0.978
10:11755531:T:CF172L0.978
10:11755533:T:AF172L0.978
10:11755533:T:GF172L0.978
10:11747360:T:CL61S0.977

dbSNP variants (sampled 300 via entrez): RS1000553969 (10:11759785 G>A,C), RS1000606317 (10:11759542 G>A,T), RS1000626996 (10:11755167 CA>C,CAA), RS1000929243 (10:11748667 C>G), RS1000980113 (10:11748841 G>A,C,T), RS1001092275 (10:11743253 T>C), RS1001211726 (10:11750839 A>C), RS1001279885 (10:11756777 C>G), RS1001285802 (10:11757423 C>T), RS1001836309 (10:11762657 G>A), RS1001868884 (10:11752016 A>G), RS1002283853 (10:11758106 T>C), RS1002311093 (10:11743880 C>T), RS1002828676 (10:11752205 G>A), RS1002895181 (10:11763715 C>A)

Disease associations

OMIM: gene MIM:620756 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

StudyTraitp-value
GCST002245_26Alzheimer’s disease (late onset)3.000000e-07
GCST002727_2Breast cancer (survival)2.000000e-06
GCST002817_12Alzheimer’s disease in APOE e4- carriers3.000000e-06
GCST004246_9Alzheimer’s disease3.000000e-08
GCST007319_8Alzheimer’s disease (late onset)2.000000e-08
GCST007320_2Alzheimer’s disease or family history of Alzheimer’s disease1.000000e-08
GCST007511_8Alzheimer’s disease (late onset)2.000000e-11
GCST009391_1582Metabolite levels5.000000e-06
GCST009391_1744Metabolite levels7.000000e-06
GCST011946_45White matter hyperintensity volume2.000000e-08
GCST011948_1White matter hyperintensity volume4.000000e-09
GCST011949_15White matter hyperintensity volume (adjusted for hypertension)2.000000e-08
GCST011951_1White matter hyperintensity volume (adjusted for hypertension)4.000000e-09

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0000714survival time
EFO:0009268family history of Alzheimer’s disease
EFO:1001870late-onset Alzheimers disease
EFO:0010349cholesteryl ester 20:5 measurement
EFO:0010348cholesteryl ester 20:4 measurement
EFO:0005665white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Benzo(a)pyrenedecreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
terbufosincreases methylation1
trichostatin Aincreases expression1
sodium arsenitedecreases expression1
nickel sulfatedecreases expression1
avobenzoneincreases expression1
di-n-butylphosphoric acidaffects expression1
tanespimycinaffects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
bisphenol Bincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
VER 155008affects cotreatment, decreases expression1
bisphenol AFincreases expression1
Norethindrone Acetateaffects cotreatment, increases expression1
Acetaminophendecreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Fonofosincreases methylation1
Estradiolaffects cotreatment, increases expression1
Fluorouracilaffects response to substance1
Nickeldecreases expression1
Parathionincreases methylation1
Rotenonedecreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Tretinoindecreases expression1
Cyclosporinedecreases expression1

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot