ECHDC2

Summary

ECHDC2 (enoyl-CoA hydratase domain containing 2, HGNC:23408) is a protein-coding gene on chromosome 1p32.3, encoding Enoyl-CoA hydratase domain-containing protein 2, mitochondrial (Q86YB7).

Predicted to enable lyase activity. Predicted to be involved in fatty acid beta-oxidation. Located in mitochondrion.

Source: NCBI Gene 55268 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 72 total
• MANE Select transcript: NM_001198961

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23408
Approved symbol	ECHDC2
Name	enoyl-CoA hydratase domain containing 2
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10948
Ensembl gene	ENSG00000121310
Ensembl biotype	protein_coding
OMIM	620724
Entrez	55268

Gene structure

Transcript identifiers

Ensembl transcripts: 61 — 39 protein_coding, 11 retained_intron, 7 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000358358, ENST00000371520, ENST00000371522, ENST00000460612, ENST00000463923, ENST00000467988, ENST00000474789, ENST00000476477, ENST00000479183, ENST00000479593, ENST00000480312, ENST00000486170, ENST00000487040, ENST00000487851, ENST00000487866, ENST00000488268, ENST00000492992, ENST00000493896, ENST00000495920, ENST00000498544, ENST00000536120, ENST00000539680, ENST00000542552, ENST00000543419, ENST00000544365, ENST00000544531, ENST00000874973, ENST00000874974, ENST00000874975, ENST00000874976, ENST00000874977, ENST00000874978, ENST00000874979, ENST00000874980, ENST00000874981, ENST00000874982, ENST00000874983, ENST00000874984, ENST00000874985, ENST00000874986, ENST00000874987, ENST00000874988, ENST00000874989, ENST00000874990, ENST00000874991, ENST00000874992, ENST00000874993, ENST00000874994, ENST00000874995, ENST00000874996, ENST00000874997, ENST00000874998, ENST00000929357, ENST00000929358, ENST00000929359, ENST00000958441, ENST00000958442, ENST00000958443, ENST00000958444, ENST00000958445, ENST00000958446

RefSeq mRNA: 4 — MANE Select: NM_001198961 NM_001198961, NM_001198962, NM_001319958, NM_018281

CCDS: CCDS55600, CCDS571, CCDS72794

Canonical transcript exons

ENST00000371522 — 10 exons

Exon	Start	End
ENSE00002278760	52921553	52921740
ENSE00003493584	52907868	52907954
ENSE00003571043	52911566	52911653
ENSE00003577171	52895910	52896597
ENSE00003604991	52904646	52904833
ENSE00003630455	52899174	52899224
ENSE00003647312	52905034	52905090
ENSE00003682877	52906519	52906611
ENSE00003723833	52911723	52911790
ENSE00003788302	52897437	52897484

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 99.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7747 / max 532.6654, expressed in 1583 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12387	7.4745	1509
12386	3.6083	1149
12385	0.5289	262
12380	0.0547	7
12383	0.0478	7
12378	0.0191	6
12379	0.0144	5
201510	0.0113	6
12381	0.0090	5
12382	0.0066	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	99.73	gold quality
right uterine tube	UBERON:0001302	99.63	gold quality
left ovary	UBERON:0002119	99.48	gold quality
right lobe of thyroid gland	UBERON:0001119	99.46	gold quality
left lobe of thyroid gland	UBERON:0001120	99.41	gold quality
right ovary	UBERON:0002118	99.41	gold quality
thyroid gland	UBERON:0002046	99.25	gold quality
adenohypophysis	UBERON:0002196	99.24	gold quality
lower esophagus mucosa	UBERON:0035834	99.24	gold quality
body of pancreas	UBERON:0001150	99.19	gold quality
endocervix	UBERON:0000458	99.14	gold quality
mucosa of stomach	UBERON:0001199	99.12	gold quality
cerebellar hemisphere	UBERON:0002245	99.08	gold quality
cerebellar cortex	UBERON:0002129	99.05	gold quality
pituitary gland	UBERON:0000007	99.01	gold quality
apex of heart	UBERON:0002098	99.00	gold quality
left uterine tube	UBERON:0001303	98.98	gold quality
right testis	UBERON:0004534	98.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.97	gold quality
body of stomach	UBERON:0001161	98.96	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.96	gold quality
body of uterus	UBERON:0009853	98.90	gold quality
right adrenal gland	UBERON:0001233	98.89	gold quality
right adrenal gland cortex	UBERON:0035827	98.88	gold quality
liver	UBERON:0002107	98.87	gold quality
left testis	UBERON:0004533	98.86	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.86	gold quality
left adrenal gland cortex	UBERON:0035825	98.83	gold quality
tibial nerve	UBERON:0001323	98.81	gold quality
minor salivary gland	UBERON:0001830	98.78	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-5061	no	3.31
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting ECHDC2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-1287-3P	99.63	66.93	492
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-1909-5P	98.94	64.01	484
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-382-3P	98.83	67.10	1074
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-127-5P	97.78	67.64	869
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-3127-5P	97.52	65.24	786
HSA-MIR-6730-3P	97.03	67.54	889
HSA-MIR-125B-2-3P	96.69	68.38	1210

Literature-anchored findings (GeneRIF, showing 1)

• ECHDC2 inhibits the proliferation of gastric cancer cells by binding with NEDD4 to degrade MCCC2 and reduce aerobic glycolysis. (PMID:38783226)

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	echdc2	ENSDARG00000016607
mus_musculus	Echdc2	ENSMUSG00000028601
rattus_norvegicus	Echdc2	ENSRNOG00000029333
drosophila_melanogaster	CG14787	FBGN0027793
drosophila_melanogaster	CG8778	FBGN0033761
drosophila_melanogaster	Dci	FBGN0035169
drosophila_melanogaster	HIPP1	FBGN0037027
drosophila_melanogaster	Srlp	FBGN0038049
drosophila_melanogaster	CG5611	FBGN0039531
caenorhabditis_elegans		WBGENE00001152
caenorhabditis_elegans		WBGENE00001154
caenorhabditis_elegans		WBGENE00007130

Paralogs (13): ECHDC1 (ENSG00000093144), ECH1 (ENSG00000104823), ECHS1 (ENSG00000127884), CDY2B (ENSG00000129873), ECHDC3 (ENSG00000134463), 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 2, mitochondrial — Q86YB7 (reviewed: Q86YB7)

All UniProt accessions (7): Q86YB7, F5GWU3, F5H0R2, F5H2K9, F5H408, F5H4W3, F6RJU0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q86YB7-1	1	yes
Q86YB7-2	2

RefSeq proteins (4): NP_001185890, NP_001185891, NP_001306887, NP_060751 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001753	Enoyl-CoA_hydra/iso	Domain
IPR014748	Enoyl-CoA_hydra_C	Homologous_superfamily
IPR018376	Enoyl-CoA_hyd/isom_CS	Conserved_site
IPR029045	ClpP/crotonase-like_dom_sf	Homologous_superfamily

Pfam: PF00378

UniProt features (10 total): site 2, modified residue 2, sequence conflict 2, transit peptide 1, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86YB7-F1	92.28	0.91

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 (2): 142 (important for catalytic activity); 162 (important for catalytic activity)

Post-translational modifications (2): 97, 97

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 200 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_LIPID_MODIFICATION, GOBP_FATTY_ACID_CATABOLIC_PROCESS, WANG_CLIM2_TARGETS_UP, JAEGER_METASTASIS_DN, NKX25_02, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, CEBPB_01, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN, GATA3_01, ROZANOV_MMP14_TARGETS_UP, GATA6_01, 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): RNA binding (GO:0003723), enoyl-CoA hydratase activity (GO:0004300), catalytic activity (GO:0003824), lyase activity (GO:0016829)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
fatty acid catabolic process	1
fatty acid ligase activity	1
fatty acid oxidation	1
primary metabolic process	1
lipid metabolic process	1
monocarboxylic acid metabolic process	1
nucleic acid binding	1
hydro-lyase activity	1
molecular_function	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1872 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ECHDC2	ALDH2	P05091	619
ECHDC2	ACAA1	P09110	610
ECHDC2	CRYL1	Q9Y2S2	582
ECHDC2	ACADVL	P49748	510
ECHDC2	VAT1L	Q9HCJ6	495
ECHDC2	MAOA	P21397	465
ECHDC2	FHIT	P49789	432
ECHDC2	DECR1	Q16698	431
ECHDC2	HPGD	P15428	431
ECHDC2	HSD17B8	Q92506	427
ECHDC2	HIBCH	Q6NVY1	421
ECHDC2	AK2	P54819	421
ECHDC2	CDC37L1	Q7L3B6	407
ECHDC2	IVD	P26440	383
ECHDC2	CCDC166	P0CW27	376

IntAct

6 interactions, top by confidence:

A	B	Type	Score
ECHDC2	NDUFS6	psi-mi:“MI:0914”(association)	0.530
ECHDC2	MAGEC1	psi-mi:“MI:0915”(physical association)	0.370
LSM8	ECHDC2	psi-mi:“MI:0915”(physical association)	0.370
ECHDC2		psi-mi:“MI:0914”(association)	0.350
ECHDC2	DBT	psi-mi:“MI:0914”(association)	0.350

BioGRID (34): AUH (Affinity Capture-MS), SLIRP (Affinity Capture-MS), TOP3A (Affinity Capture-MS), UQCC1 (Affinity Capture-MS), NDUFS6 (Affinity Capture-MS), IBA57 (Affinity Capture-MS), CTU1 (Affinity Capture-MS), DNLZ (Affinity Capture-MS), AUH (Affinity Capture-MS), NDUFS6 (Affinity Capture-MS), ALAS1 (Affinity Capture-MS), DNLZ (Affinity Capture-MS), SLIRP (Affinity Capture-MS), MMAB (Affinity Capture-MS), CTU1 (Affinity Capture-MS)

ESM2 similar proteins: A0A162J448, A5JTM5, D3YZG8, D3ZUA0, F1LU71, F4JLP5, F4JML5, F6ZFR0, F9XMX6, G4N954, O49809, O69762, O85078, P07896, P13995, P18155, P29147, P55100, Q02337, Q02338, Q08426, Q0P5C2, Q13825, Q1ERI2, Q2TBT3, Q32LQ3, Q39659, Q3TLP5, Q42843, Q4PEN0, Q54HG7, Q589W8, Q5R5M8, Q5XF59, Q5ZKA5, Q6NL24, Q80XN0, Q86YB7, Q8K009, Q8LK61

Diamond homologs: A0A481WNM8, A0KEL1, A0KV76, A1ADI8, A1JK30, A1RI92, A1S7L6, A3D684, A3QFP3, A4TM82, A4WCW6, A4Y897, A4YI89, A5F2P2, A5WH99, A6WQ25, A7FGK1, A7ZPF8, A8A2L0, A8ADP2, A9N453, B0TL21, B1IXA5, B1LME7, B1X9L4, B2TWV4, B4SZR0, B4TCA8, B4TQC2, B5EZR9, B5FPN1, B5R3R9, B5RCL3, B5XVW2, B5YXY4, B6I6Q4, B7LBJ5, B7LLD0, B7M6M2, B7MGV7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1678 predictions. Top by Δscore:

Variant	Effect	Δscore
1:52904838:CAGGA:C	acceptor_gain	1.0000
1:52911561:CCTA:C	donor_loss	1.0000
1:52911562:CTAC:C	donor_loss	1.0000
1:52911563:TAC:T	donor_loss	1.0000
1:52911564:A:C	donor_loss	1.0000
1:52911654:C:CC	acceptor_gain	1.0000
1:52896593:ATATT:A	acceptor_gain	0.9900
1:52896594:TATT:T	acceptor_gain	0.9900
1:52896596:TT:T	acceptor_gain	0.9900
1:52896597:TC:T	acceptor_loss	0.9900
1:52896598:C:CC	acceptor_gain	0.9900
1:52896598:CTGCA:C	acceptor_loss	0.9900
1:52896599:T:G	acceptor_loss	0.9900
1:52904839:A:T	acceptor_gain	0.9900
1:52906513:CAGTA:C	donor_loss	0.9900
1:52906514:AGTAC:A	donor_loss	0.9900
1:52906515:GTA:G	donor_loss	0.9900
1:52906516:TACCT:T	donor_loss	0.9900
1:52906517:A:G	donor_loss	0.9900
1:52906518:C:CG	donor_loss	0.9900
1:52906607:GGCTG:G	acceptor_gain	0.9900
1:52906609:CTG:C	acceptor_gain	0.9900
1:52906612:C:CC	acceptor_gain	0.9900
1:52907860:ATCCT:A	donor_loss	0.9900
1:52907862:CCT:C	donor_loss	0.9900
1:52907863:CTCAC:C	donor_loss	0.9900
1:52907864:TCA:T	donor_loss	0.9900
1:52907865:CACCG:C	donor_loss	0.9900
1:52907866:A:AC	donor_gain	0.9900
1:52907866:A:G	donor_loss	0.9900

AlphaMissense

1840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:52896532:A:C	F289L	0.996
1:52896532:A:T	F289L	0.996
1:52896534:A:G	F289L	0.996
1:52905063:T:A	E162V	0.995
1:52896556:G:C	F281L	0.994
1:52896556:G:T	F281L	0.994
1:52896558:A:G	F281L	0.994
1:52911573:G:C	F90L	0.994
1:52911573:G:T	F90L	0.994
1:52911575:A:G	F90L	0.994
1:52905062:C:A	E162D	0.993
1:52905062:C:G	E162D	0.993
1:52911572:A:G	C91R	0.993
1:52906533:T:A	D148V	0.992
1:52906590:A:T	I129N	0.992
1:52906587:G:T	A130E	0.991
1:52904782:A:G	L189P	0.990
1:52904787:C:A	K187N	0.990
1:52904787:C:G	K187N	0.990
1:52906537:A:G	C147R	0.990
1:52906535:A:C	C147W	0.989
1:52906536:C:T	C147Y	0.989
1:52906551:T:A	E142V	0.989
1:52911574:A:G	F90S	0.989
1:52906575:C:T	G134E	0.988
1:52911571:C:T	C91Y	0.988
1:52899198:T:A	K243N	0.987
1:52899198:T:G	K243N	0.987
1:52905051:C:T	G166E	0.987
1:52906569:G:T	A136D	0.987

dbSNP variants (sampled 300 via entrez): RS1000106647 (1:52906921 C>T), RS1000110775 (1:52899712 C>T), RS1000158891 (1:52903813 C>G), RS1000175850 (1:52910920 C>T), RS1000414877 (1:52897125 C>G), RS1000505624 (1:52900022 C>G), RS1000547626 (1:52910677 C>T), RS1000596377 (1:52905340 C>T), RS1000700313 (1:52911707 G>A), RS1000711382 (1:52898351 G>T), RS1000759167 (1:52918334 T>C,G), RS1000787357 (1:52896924 T>C), RS1000899928 (1:52912474 C>T), RS1001114516 (1:52905307 TG>T), RS1001228651 (1:52898639 C>T)

Disease associations

OMIM: gene MIM:620724 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects expression, decreases expression, increases methylation	4
Acetaminophen	decreases expression	3
Valproic Acid	affects methylation, decreases expression, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Benzo(a)pyrene	decreases expression	2
Cisplatin	affects expression, affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
bufotalin	decreases expression	1
bisphenol A	decreases methylation	1
arsenite	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
belinostat	decreases expression	1
ICG 001	increases expression	1
Grape Seed Proanthocyanidins	decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Decitabine	affects expression	1
Sunitinib	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Catechin	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Nickel	decreases expression	1
Niclosamide	decreases expression	1

Clinical trials (associated diseases)

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