ECHDC3

protein-coding

enoyl-CoA hydratase domain containing 3

Gene summary

Predicted to enable enoyl-CoA hydratase activity. Involved in positive regulation of cellular response to insulin stimulus. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024693.5

Inheritance

—

ClinVar variants

U:37B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr10:11,742,366-11,764,070

External References & Databases

Ensembl (ENSG00000134463)

Transcript & Mutation Effects

hg38 • Region Span ~21.7 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 ECHDC3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024693.5. 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						0
missense			35 clinvar	3 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	37	3	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024693.5	RefSeq	NP_078969.3	5	MANE Select
ENST00000379215.9	Ensembl	ENSP00000368517.4	5	MANE Select
ENST00000420401.5	Ensembl	ENSP00000405584.1	4	Standard
ENST00000422887.1	Ensembl	ENSP00000398429.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fatty Acid Biosynthesis
Liver steatosis AOP

Molecular Function

catalytic activity

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379215
Coding exons: 5
Length: 21705
Individuals with no LoFs: 125485
Homozygous LoFs: 1
Heterozygous LoFs: 262
Defined: 125748
p: 0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.190	166	159	1.04	0.00000957	1925
Missense (PolyPhen)		56	58.884	0.95102		671
Synonymous	0.0984	68	69.0	0.985	0.00000474	632
Loss of Function	-0.0563	8	7.83	1.02	3.30e-7	115

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00096	0.00095	rare
Ashkenazi Jewish	0.0078	0.0078	notable
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.0033	0.0032	notable
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.164

Intolerance Scores

RVIS EVS: 0.42
RVIS percentile EVS: 77.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.195

Gene Damage Prediction

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