EHHADH
protein-codingenoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase, the group of MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is a bifunctional enzyme and is one of the four enzymes of the peroxisomal beta-oxidation pathway. The N-terminal region of the encoded protein contains enoyl-CoA hydratase activity while the C-terminal region contains 3-hydroxyacyl-CoA dehydrogenase activity. Defects in this gene are a cause of peroxisomal disorders such as Zellweger syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
- ECHD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~91.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014275
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014275
Submitter: ClinGen
The relationship between *EHHADH* and Fanconi renotubular syndrome 3, an autosomal dominant disorder, was evaluated using the ClinGen Clinical Validity Framework as of March, 2023. *EHHADH* encodes enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase, a bifunctional enzyme (a.k.a L-bifunctional protein) and is one of the four enzymes of the peroxisomal beta-oxidation pathway. A single heterozygous missense variant in this gene has been reported in the literature to cause Fanconi renotubular syndrome 3. *EHHADH* was first reported in relation to autosomal dominant Fanconi renotubular syndrome 3 in 2014. (Klootwijk et al, PMID: 24401050). To the best of our knowledge, the Glu3Lys missense variant is the only recurrent pathogenic variant identified in this gene. Summary of Case Level Data (4.1 points): The same heterozygous missense variant (Glu3Lys) has been reported in 5 probands across 5 publications (PMIDs: 24401050, 1627757, 40800210, 40242153, 41117969). An additional publication not ndexed in PubMed (Seaby et al, 2017) notes a de novo Glu3Lys variant in EHHADH identified by trio WES adding 1 pt to the case-level evidence. Functional evidence shows that this primarily peroxisomal protein is mistargeted to the mitochondria as the variant, Glu3Lys, creates a mitochondrial-targeting signal and interferes with mitochondrial function by interacting with the mitochondrial trifunctional protein (PMID: 24401050, 27160910). The mechanism for disease is expected to be dominant negative. Summary of experimental data (1 point): This gene-disease association is supported by limited experimental evidence. The *EHHADH* protein is shown to be expressed in the renal proximal tubules, which are tissues relevant to the disease (PMIDs: 24401050, 10336479). In addition, experiments with the variant expressed in proximal tubular cells show functional impairment and confirm mistargeting of the protein to the mitochondria (PMIDs: 24401050, 10336479). In summary, there is limited evidence to support the gene-disease relationship of *EHHADH* and Fanconi renotubular syndrome 3. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This gene-disease pair was originally evaluated by the Peroxisomal GCEP on Mar 3, 2023. It was reevaluated on Mar 6, 2026 (SOP v12). Although four new cases were published (PMIDs: 40800210, 40242153, 41117969, Seaby et al, 2017), the classification did not change.
Inheritance Pattern: AD
Disease ID:MONDO:0014275
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007600
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0014275
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Renal
Intervention: Renal
Rationale: Manifestations in the described individuals can include severe rickets, and early knowledge may allow medical/dietary interventions (eg, with calcitriol, and phosphate supplementation) to prevent (and treat) this complication
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EHHADH variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001966.4. 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 | 15 | 41 | 3 | 59 | ||
| missense | 2 | 167 | 31 | 8 | 208 | |
| nonsense | 13 | 13 | ||||
| start loss | 0 | |||||
| frameshift | 13 | 2 | 15 | |||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 2 | 212 | 74 | 11 | 299 |
Highest pathogenic variant AF is 0.000016727796
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001957.2 | 7 | MANE Select | |
| Ensembl | ENSP00000231887.3 | 7 | MANE Select | |
| RefSeq | NP_001159887.1 | 5 | Standard | |
| Ensembl | ENSP00000396798.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tryptophan metabolism - Homo sapiens (human)
- Butanoate metabolism - Homo sapiens (human)
- beta-Alanine metabolism - Homo sapiens (human)
- Lysine degradation - Homo sapiens (human)
- Propanoate metabolism - Homo sapiens (human)
Biological Process
- internal protein amino acid acetylation
- protein targeting to peroxisome
- fatty acid beta-oxidation
- fatty acid beta-oxidation using acyl-CoA oxidase
Molecular Function
- 3-hydroxyacyl-CoA dehydrogenase activity
- dodecenoyl-CoA delta-isomerase activity
- enoyl-CoA hydratase activity
- signaling receptor binding
- protein binding
Cellular Component
- peroxisome
- peroxisomal matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000231887
- Coding exons
- 7
- Length
- 91367
- Individuals with no LoFs
- 125497
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 248
- Defined
- 125747
- p
- 0.000995
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0259 | 394 | 393 | 1.00 | 0.0000204 | 4636 |
| Missense (PolyPhen) | 139 | 137.71 | 1.0094 | 1666 | ||
| Synonymous | 0.688 | 139 | 150 | 0.928 | 0.00000765 | 1492 |
| Loss of Function | 1.68 | 19 | 28.7 | 0.662 | 0.00000156 | 366 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00087 | 0.00080 | rare |
| Latino/Admixed American | 0.00046 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.0010 | 0.0010 | notable |
| South Asian | 0.0031 | 0.0030 | notable |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: Fanconi renotubular syndrome 3 (FRTS3) [MIM:615605]: A disease due to a generalized dysfunction of the proximal kidney tubule resulting in decreased solute and water reabsorption. Patients have polydipsia and polyuria with phosphaturia, glycosuria and aminoaciduria. They may develop hypophosphatemic rickets or osteomalacia, acidosis and a tendency toward dehydration. Some eventually develop renal insufficiency. {ECO:0000269|PubMed:24401050}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.408
Intolerance Scores
- LoFtool
- 0.325
- RVIS EVS
- 2.27
- RVIS percentile EVS
- 98.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.224
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |