ECHDC1

protein-coding

ethylmalonyl-CoA decarboxylase 1

Gene summary

Predicted to enable carboxy-lyase activity. Predicted to be involved in fatty acid beta-oxidation. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001002030.2

Inheritance

—

ClinVar variants

P:2U:29B:1

Top phenotype

Deficiency of butyryl-CoA dehydrogenase

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr6:127,288,712-127,343,609

External References & Databases

Ensembl (ENSG00000093144)

Transcript & Mutation Effects

hg38 • Region Span ~54.9 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 ECHDC1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 27

Deficiency of butyryl-CoA dehydrogenaseTotal: 3

ECHDC1-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001002030.2. 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
missense		1 clinvar	28 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	0	2	29	1	0	32

Highest pathogenic variant AF is 0.000042317348

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001002030.2	RefSeq	NP_001002030.1	5	MANE Select
ENST00000454859.8	Ensembl	ENSP00000401751.3	5	MANE Select
NM_001105544.2	RefSeq	NP_001099014.1	4	Standard
NM_001105545.2	RefSeq	NP_001099015.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Propanoate metabolism - Homo sapiens (human)
Fatty Acid Biosynthesis
Liver steatosis AOP

Biological Process

fatty acid beta-oxidation

Molecular Function

enoyl-CoA hydratase activity
carboxy-lyase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000531967
Coding exons: 6
Length: 54900
Individuals with no LoFs: 125623
Homozygous LoFs: 0
Heterozygous LoFs: 118
Defined: 125741
p: 0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.652	136	159	0.855	0.00000765	1993
Missense (PolyPhen)		34	45.093	0.754		534
Synonymous	-1.11	69	58.2	1.19	0.00000306	601
Loss of Function	0.138	13	13.5	0.960	5.73e-7	187

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00043	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0021	0.0021	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00049	0.00049	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Decarboxylases ethylmalonyl-CoA decarboxylase, a potentially toxic metabolite, to form butyryl-CoA, suggesting it might be involved in metabolite proofreading. Also has methylmalonyl-CoA decarboxylase activity at lower level. {ECO:0000269|PubMed:22016388}.;

Recessive Scores

pRec: 0.0974

Intolerance Scores

LoFtool: 0.587
RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0688

Gene Damage Prediction

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