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 enoyl-CoA hydratase activity. Predicted to be involved in fatty acid beta-oxidation. Located in mitochondrion.

Source: NCBI Gene 55268 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• Clinical variants (ClinVar): 72 total
• GTEx eGene: eQTL in 38 tissues, sQTL in 40 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.03 (unconstrained)
• MANE Select transcript: NM_001198961
• Notable: 72 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 152 — 78 nonsense_mediated_decay, 56 protein_coding, 11 retained_intron, 7 protein_coding_CDS_not_defined

MANE Select: ENST00000371522

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 6, TSL 3: 10, TSL 4: 1, TSL 5: 5

ENST00000371522, ENST00000358358, ENST00000371520, 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, ENST00000975709, ENST00000975710, ENST00000975711, ENST00000975712, ENST00000975713, ENST00000975714, ENST00000975715, ENST00000975716, ENST00000975717, ENST00000975718, ENST00000975719, ENST00000975720, ENST00000975721, ENST00000975722, ENST00000975723, ENST00000975724, ENST00000975725, ENST00000975726, ENST00000975727, ENST00000975728, ENST00000975729, ENST00000975733, ENST00000975734, ENST00000975735, ENST00000975738, ENST00000975739, ENST00000975740, ENST00000975741, ENST00000975743, ENST00000975744, ENST00000975745, ENST00000975746, ENST00000975747, ENST00000975748, ENST00000975749, ENST00000975750, ENST00000975751, ENST00000975752, ENST00000975753, ENST00000975754, ENST00000975755, ENST00000975757, ENST00000975759, ENST00001011178, ENST00001011179, ENST00001011180, ENST00001011181, ENST00001011183, ENST00001011185, ENST00001011186, ENST00001011187, ENST00001011188, ENST00001011189, ENST00001011190, ENST00001011191, ENST00001011193, ENST00001011194, ENST00001011195, ENST00001011196, ENST00001011197, ENST00001011198, ENST00001011202, ENST00001011204, ENST00001011205, ENST00001011206, ENST00001011207, ENST00001011208, ENST00001011209, ENST00001011210, ENST00001011211, ENST00001011212, ENST00001011214, ENST00001011215, ENST00001011216, ENST00001011217, ENST00001011219, ENST00001011220, ENST00001011221, ENST00001065313, ENST00001094239, ENST00001094240, ENST00001094241, ENST00001094242, ENST00001094243, ENST00001094244, ENST00001094245, ENST00001094246, ENST00001094247, ENST00001119518, ENST00001119519, ENST00001145572

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.

Highest expression (Bgee): lobe of liver, uterine tube, ovary, lobe of thyroid gland, thyroid gland.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ECHDC2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 38 tissues and its splicing (sQTL) in 40 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 78 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Nerve Tibial	sqtl	5.9e-73	+2.44	1:52926925:G:T
Whole Blood	eqtl	4.7e-43	+0.26	1:52927236:A:G
Testis	sqtl	1.8e-36	+3.51	1:52698188:G:T
Artery Aorta	sqtl	4.3e-35	+1.98	1:52878401:A:G
Thyroid	sqtl	7.4e-31	+2.00	1:52884262:C:T
Brain Cerebellar Hemisphere	sqtl	3.5e-25	+1.55	1:52899236:CAA:C
Colon Sigmoid	sqtl	7.4e-24	+2.52	1:52884262:C:T
Brain Cerebellum	sqtl	1.9e-23	+1.61	1:52899236:CAA:C
Artery Tibial	sqtl	3.2e-23	+2.02	1:52935226:A:G
Pituitary	sqtl	4.5e-22	+2.49	1:52808091:G:A
Esophagus Muscularis	sqtl	1.7e-19	+1.94	1:52884262:C:T
Skin Not Sun Exposed Suprapubic	sqtl	2.6e-19	+2.57	1:52711697:G:A
Prostate	sqtl	1.3e-18	+3.28	1:52714484:C:G
Nerve Tibial	eqtl	5.8e-18	+0.45	1:52966722:A:G
Esophagus Mucosa	sqtl	8.4e-18	+2.43	1:52724640:C:T
Stomach	sqtl	9.2e-18	+1.71	1:52884262:C:T
Lung	sqtl	1.3e-17	+1.52	1:52884262:C:T
Colon Transverse	sqtl	4.6e-17	+2.12	1:52698188:G:T
Adipose Subcutaneous	sqtl	1.2e-16	+1.69	1:52935226:A:G
Skin Sun Exposed Lower leg	sqtl	8.7e-16	+2.05	1:52698188:G:T

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

showing 100 of 285 tissues 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
metanephros cortex	UBERON:0010533	98.78	gold quality
lower esophagus	UBERON:0013473	98.78	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.78	gold quality
left adrenal gland	UBERON:0001234	98.77	gold quality
fundus of stomach	UBERON:0001160	98.75	gold quality
adrenal cortex	UBERON:0001235	98.75	gold quality
ectocervix	UBERON:0012249	98.74	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.71	gold quality
right atrium auricular region	UBERON:0006631	98.58	gold quality
esophagus	UBERON:0001043	98.56	gold quality
transverse colon	UBERON:0001157	98.54	gold quality
omental fat pad	UBERON:0010414	98.47	gold quality
right coronary artery	UBERON:0001625	98.46	gold quality
peritoneum	UBERON:0002358	98.46	gold quality
saliva-secreting gland	UBERON:0001044	98.44	gold quality
esophagus mucosa	UBERON:0002469	98.44	gold quality
skin of abdomen	UBERON:0001416	98.43	gold quality
cerebellum	UBERON:0002037	98.36	gold quality
right lung	UBERON:0002167	98.34	gold quality
adipose tissue of abdominal region	UBERON:0007808	98.34	gold quality
descending thoracic aorta	UBERON:0002345	98.29	gold quality
small intestine	UBERON:0002108	98.27	gold quality
ascending aorta	UBERON:0001496	98.21	gold quality
skin of leg	UBERON:0001511	98.21	gold quality
thoracic aorta	UBERON:0001515	98.20	gold quality
stomach	UBERON:0000945	98.14	gold quality
coronary artery	UBERON:0001621	98.11	gold quality
left coronary artery	UBERON:0001626	98.11	gold quality
prostate gland	UBERON:0002367	98.10	gold quality
cardiac atrium	UBERON:0002081	98.06	gold quality
adrenal gland	UBERON:0002369	98.04	gold quality
adult mammalian kidney	UBERON:0000082	98.03	gold quality
aorta	UBERON:0000947	98.01	gold quality
mouth mucosa	UBERON:0003729	97.97	gold quality
popliteal artery	UBERON:0002250	97.91	gold quality
tibial artery	UBERON:0007610	97.90	gold quality
mucosa of transverse colon	UBERON:0004991	97.87	gold quality
subcutaneous adipose tissue	UBERON:0002190	97.86	gold quality
vagina	UBERON:0000996	97.73	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.73	gold quality
rectum	UBERON:0001052	97.64	gold quality
heart left ventricle	UBERON:0002084	97.64	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.60	gold quality
cardiac ventricle	UBERON:0002082	97.50	gold quality
heart	UBERON:0000948	97.40	gold quality
granulocyte	CL:0000094	97.29	gold quality
gall bladder	UBERON:0002110	97.29	gold quality
upper lobe of left lung	UBERON:0008952	97.23	gold quality
colon	UBERON:0001155	97.17	gold quality
intestine	UBERON:0000160	97.15	gold quality
renal medulla	UBERON:0000362	97.08	gold quality
zone of skin	UBERON:0000014	97.00	gold quality
parotid gland	UBERON:0001831	96.94	gold quality
large intestine	UBERON:0000059	96.92	gold quality
nucleus accumbens	UBERON:0001882	96.89	gold quality
adipose tissue	UBERON:0001013	96.88	gold quality
ovary	UBERON:0000992	96.85	gold quality
testis	UBERON:0000473	96.56	gold quality
kidney	UBERON:0002113	96.56	gold quality
uterine cervix	UBERON:0000002	96.54	gold quality
colonic epithelium	UBERON:0000397	96.49	gold quality
upper lobe of lung	UBERON:0008948	96.49	gold quality
cardia of stomach	UBERON:0001162	96.46	gold quality
caudate nucleus	UBERON:0001873	96.45	gold quality
seminal vesicle	UBERON:0000998	96.43	gold quality
duodenum	UBERON:0002114	96.43	gold quality
cortex of kidney	UBERON:0001225	96.28	gold quality
gastrocnemius	UBERON:0001388	96.25	gold quality
spleen	UBERON:0002106	96.13	gold quality
amygdala	UBERON:0001876	96.12	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

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Liver	tissue	81.4	high
Skeletal muscle	tissue	28.1	not detected
Tongue	tissue	25.0
Kidney	tissue	23.0	high
Vagina	tissue	15.9	not detected
Duodenum	tissue	15.7	medium
Pituitary gland	tissue	15.5
Parathyroid gland	tissue	13.5	medium
Thyroid gland	tissue	12.7	medium
Heart muscle	tissue	12.2	not detected
Spinal cord	tissue	12.2
Adipose tissue	tissue	12.0	not detected
Superior colliculi	tissue	11.4
Small intestine	tissue	11.4	low
Salivary gland	tissue	11.0	not detected
Olfactory bulb	tissue	10.0
Prostate	tissue	9.9	medium
Stomach 1	tissue	9.8	medium
Adrenal gland	tissue	9.8	medium
Medulla oblongata	tissue	9.4
Ovary	tissue	8.2	not detected
Substantia nigra	tissue	8.2
Seminal vesicle	tissue	7.9	low
Cerebral cortex	tissue	7.7	not detected
Occipital cortex	tissue	7.7
Somatosensory cortex	tissue	7.6
Fallopian tube	tissue	7.5	low
Cerebellum	tissue	7.4	not detected
Hippocampal formation	tissue	7.2
Entorhinal cortex	tissue	7.2
Temporal cortex	tissue	7.2
Insular cortex	tissue	7.0
Colon	tissue	6.8	medium
Amygdala	tissue	6.8
Retrosplenial and cingulate cortex	tissue	6.6
Retrosplenial cortex	tissue	6.6
Midbrain	tissue	6.5
Esophagus	tissue	6.3	not detected
Prefrontal cortex	tissue	6.2
Pons	tissue	6.1
Periaqueductal gray	tissue	6.1
Motor cortex	tissue	5.9
Breast	tissue	5.8	not detected
Thalamus	tissue	5.8
Lung	tissue	5.8	not detected
Basal ganglia	tissue	5.7	not detected
Hypothalamus	tissue	5.7
Epididymis	tissue	5.2	medium
Ventral forebrain	tissue	5.2
Choroid plexus	tissue	5.1
Corpus callosum	tissue	5.0
Putamen	tissue	4.9
Retina	tissue	4.7
Gallbladder	tissue	4.7	medium
Cervix	tissue	4.6	not detected
Urinary bladder	tissue	4.5	not detected
Septum	tissue	4.3
Placenta	tissue	4.2	not detected
Frontal cortex	tissue	3.7
Pancreas	tissue	3.5	not detected

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Blood vessel (18.0), Ventral spinal cord (12.2), Dorsal spinal cord (11.6), Subiculum (6.6), Ventral hippocampus (5.8).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ECHDC2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

30 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 1.24e-07, LOEUF 1.03, missense Z 0.774 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000371522 — one region, missense o/e 0.98.

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)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2	A1KN36	100.0%	Diamond
Mycobacterium tuberculosis H37Ra	A5U753	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7	A9MYJ5	100.0%	Diamond
Escherichia coli ATCC 8739	B1IRE0	100.0%	Diamond
Proteus mirabilis HI4320	B4EY26	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Heidelberg str. SL476	B4TIG9	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633	B4TWR3	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Paratyphi A str. AKU_12601	B5BL54	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Agona str. SL483	B5F749	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853	B5FHG4	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Enteritidis str. P125109	B5R1Q9	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91	B5RGA4	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Paratyphi C str. RKS4594	C0Q4L2	100.0%	Diamond
Escherichia coli K-12	P0ABU0	100.0%	Diamond
Escherichia coli CFT073	P0ABU1	100.0%	Diamond
Mycobacterium tuberculosis variant bovis AF2122/97	P64017	100.0%	Diamond
Mycobacterium tuberculosis CDC1551	P9WNN2	100.0%	Diamond
Mycobacterium tuberculosis H37Rv	P9WNN3	100.0%	Diamond
Escherichia coli 536	Q0TLV3	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67	Q57TJ1	100.0%	Diamond
Staphylococcus aureus subsp. aureus COL	Q5HH38	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150	Q5PIL1	100.0%	Diamond
Staphylococcus aureus subsp. aureus MSSA476	Q6GAG7	100.0%	Diamond
Staphylococcus aureus subsp. aureus MRSA252	Q6GI37	100.0%	Diamond
Staphylococcus aureus subsp. aureus N315	Q7A6A9	100.0%	Diamond
Proteus sp. LE138	Q8GB17	100.0%	Diamond
Staphylococcus aureus subsp. aureus MW2	Q8NXA0	100.0%	Diamond
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Q8ZRX5	100.0%	Diamond
Staphylococcus aureus subsp. aureus Mu50	Q99V48	100.0%	Diamond
Mycobacterium avium 104	A0QJH8	99.6%	Diamond
Escherichia coli SMS-3-5	B1LFW9	99.6%	Diamond
Salmonella enterica subsp. enterica serovar Newport str. SL254	B4T6J5	99.6%	Diamond
Arthrobacter sp.	O85078	99.6%	Diamond
Shigella flexneri	P59395	99.6%	Diamond
Mycobacterium avium subsp. paratuberculosis K-10	Q73VC7	99.6%	Diamond
Salmonella enterica subsp. enterica serovar Typhi	Q8Z9L5	99.6%	Diamond
Escherichia coli O157:H7	Q8XA35	99.2%	Diamond
Pongo abelii	Q5RFG0	97.9%	Diamond
Staphylococcus haemolyticus JCSC1435	Q4L549	97.0%	Diamond
Citrobacter koseri ATCC BAA-895	A8ALR7	95.8%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
ZYG11A	protein-coding	440590
SCP2	protein-coding	6342
ZYG11B	protein-coding	79699
PODN	protein-coding	127435
SLC1A7	protein-coding	6512

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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Metabolic proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): mitochondria

Antibody reliability (HPA): IH enhanced · IF approved

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)

Position	Role
142	important for catalytic activity
162	important for catalytic activity

Post-translational modifications (2)

Type	Positions
N6-acetyllysine	97
N6-succinyllysine	97

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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

12 GO namespaces:

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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 8 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
mitochondrion	CC	high-throughput

Protein interactions and networks

STRING

showing 15 of 1,208 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ECHDC2	IVD	P26440	422
ECHDC2	DECR1	Q16698	420
ECHDC2	CRAT	P43155	403
ECHDC2	ACAA1	P09110	388
ECHDC2	DRAP1	Q14919	366
ECHDC2	AASDH	Q4L235	358
ECHDC2	ACADL	P28330	355
ECHDC2	GCDH	Q92947	339
ECHDC2	DLST	P36957	320
ECHDC2	CDC37L1	Q7L3B6	314
ECHDC2	ALDH6A1	Q02252	310
ECHDC2	ACACB	O00763	307
ECHDC2	ACAD11	Q709F0	306
ECHDC2	HADH	Q16836	304
ECHDC2	PECR	Q9BY49	299

IntAct

Human interaction partners of ECHDC2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

4 partners by confidence:

Partner	Interaction type	MIscore	Records
NDUFS6	association	0.530	1
LSM8	physical association	0.370	1
MAGEC1	physical association	0.370	1
DBT	association	0.350	1

BioGRID (34 interactions; top human partners by supporting records): AUH (Affinity Capture-MS; 3 records), CTU1 (Affinity Capture-MS; 3 records), DNLZ (Affinity Capture-MS; 3 records), NDUFS6 (Affinity Capture-MS; 3 records), SLIRP (Affinity Capture-MS; 3 records), TOP3A (Affinity Capture-MS; 3 records), ALAS1 (Affinity Capture-MS), APP (Reconstituted Complex), BIRC6 (Affinity Capture-MS), CYP24A1 (Affinity Capture-MS), DBT (Affinity Capture-MS), HNRNPA2B1 (Cross-Linking-MS (XL-MS)), HNRNPL (Affinity Capture-RNA), IBA57 (Affinity Capture-MS), IVD (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for ECHDC2: 72 ClinVar records (0 pathogenic / likely pathogenic).

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

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 43 predictions of 877):

Position(s)	Effect	Δscore	Sites
1:52911564–52911565	donor_loss	1.0000	5
1:52896598–52896599	acceptor_loss	0.9900	6
1:52904839	acceptor_gain	0.9900
1:52906517–52906518	donor_loss	0.9900	6
1:52907866–52907867	donor_loss	0.9900	6
1:52911654–52911655	acceptor_loss	0.9900	5
1:52921551–52921552	donor_loss	0.9900	6
1:52904644–52904645	donor_loss	0.9800	6
1:52904835	acceptor_loss	0.9800
1:52904842	acceptor_gain	0.9800

AlphaMissense

711 missense substitutions predicted likely pathogenic (of 1,840 scored), across 189 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
D148	8	0.970	0.992
F90	8	0.963	0.994
D273	8	0.960	0.983
F281	8	0.949	0.994
N54	8	0.940	0.987
D95	8	0.911	0.975
D133	8	0.808	0.928
E162	7	0.974	0.995
F289	7	0.974	0.996
E142	7	0.971	0.989
E261	7	0.948	0.977
F110	7	0.918	0.981
C91	7	0.915	0.993
F191	7	0.900	0.972
C147	7	0.886	0.990
S84	7	0.882	0.986
E276	7	0.876	0.936
M102	7	0.826	0.951
Q175	7	0.809	0.957
F124	7	0.803	0.912

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	5.05e-07
Liver Hepatocellular Carcinoma (TCGA)	favorable	0.000862

Disease associations

OMIM: gene MIM:620724 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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	increases abundance, decreases expression, affects cotreatment	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	affects cotreatment, decreases expression	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	increases abundance, affects expression	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)

Via MONDO — disease-level, not drug-specific.