ECHDC2

protein-coding

enoyl-CoA hydratase domain containing 2

Gene summary

Predicted to enable enoyl-CoA hydratase activity. Predicted to be involved in fatty acid beta-oxidation. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001198961.2

Inheritance

—

ClinVar variants

U:60B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr1:52,895,910-52,927,212

External References & Databases

Ensembl (ENSG00000121310)

Transcript & Mutation Effects

hg38 • Region Span ~31.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ECHDC2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001198961.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	60	3	0	63

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 190 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198961.2	RefSeq	NP_001185890.1	10	MANE Select
ENST00000371522.9	Ensembl	ENSP00000360577.4	10	MANE Select
NM_001198962.1	RefSeq	NP_001185891.1	8	Standard
NM_001319958.2	RefSeq	NP_001306887.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fatty Acid Biosynthesis
Liver steatosis AOP
Butanoate metabolism

Biological Process

fatty acid beta-oxidation

Molecular Function

enoyl-CoA hydratase activity

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371522
Coding exons: 10
Length: 31229
Individuals with no LoFs: 124953
Homozygous LoFs: 0
Heterozygous LoFs: 795
Defined: 125748
p: 0.00317

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0937	185	189	0.981	0.0000120	1810
Missense (PolyPhen)		82	90.464	0.90643		811
Synonymous	-0.141	79	77.4	1.02	0.00000462	658
Loss of Function	0.685	17	20.3	0.836	0.00000149	170

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00082	0.00080	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0.0032	0.0031	notable
East Asian	0.0020	0.0020	notable
Finnish	0.0013	0.0012	notable
European (Non-Finnish)	0.0052	0.0050	notable
South Asian	0.0024	0.0023	notable
Other	0.0035	0.0034	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.181

Intolerance Scores

LoFtool: 0.809
RVIS EVS: 0.06
RVIS percentile EVS: 58.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.146

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium