EHHADH

protein-coding

enoyl-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]

Previous symbols:
  • ECHD

MANE transcript

NM_001966.4

Inheritance

AD

ClinVar variants

P:2U:212B:85

Top phenotype

Fanconi renotubular syndrome 3

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr3:185,190,624-185,281,990

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~91.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Fanconi renotubular syndrome 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014275

Submitter: PanelApp Australia

Fanconi renotubular syndrome 3LIMITED

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.

Fanconi renotubular syndrome 3LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014275

Submitter: Labcorp Genetics (formerly Invitae)

primary Fanconi syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007600

Submitter: Orphanet

Fanconi renotubular syndrome 3LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014275

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Fanconi renotubular syndrome 3AD

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

Refs: 1627757; 24401050Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EHHADH variants in ClinVar

8 Conditions Cataloged
EHHADH-related disorderTotal: 161
not specifiedTotal: 135
not providedTotal: 123
Fanconi renotubular syndrome 3Total: 20
Chronic kidney diseaseTotal: 2
EHHADH-related disordersTotal: 1
Fanconi renotubular syndrome 1Total: 1
CholestasisTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
15
clinvar
41
clinvar
3
clinvar
59
missense
2
clinvar
167
clinvar
31
clinvar
8
clinvar
208
nonsense
13
clinvar
13
start loss
0
frameshift
13
clinvar
2
clinvar
15
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total022127411299

Highest pathogenic variant AF is 0.000016727796

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001966.4RefSeqNP_001957.27MANE Select
ENST00000231887.8EnsemblENSP00000231887.37MANE Select
NM_001166415.2RefSeqNP_001159887.15Standard
ENST00000440662.1EnsemblENSP00000396798.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.02593943931.000.00002044636
Missense (PolyPhen)139137.711.00941666
Synonymous0.6881391500.9280.000007651492
Loss of Function1.681928.70.6620.00000156366

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000870.00080rare
Latino/Admixed American0.000460.00046rare
Ashkenazi Jewish00.0absent
East Asian0.000270.00027rare
Finnish0.000140.00014rare
European (Non-Finnish)0.00100.0010notable
South Asian0.00310.0030notable
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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