ECI1
protein-codingenoyl-CoA delta isomerase 1
Gene summary
This gene encodes a member of the hydratase/isomerase superfamily. The protein encoded is a key mitochondrial enzyme involved in beta-oxidation of unsaturated fatty acids. It catalyzes the transformation of 3-cis and 3-trans-enoyl-CoA esters arising during the stepwise degradation of cis-, mono-, and polyunsaturated fatty acids to the 2-trans-enoyl-CoA intermediates. Alternatively spliced transcript variants have been described. [provided by RefSeq, May 2010]
- DCI
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.9 kbGenCC 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 ECI1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001919.4. 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 | 2 | 2 | ||||
| missense | 74 | 3 | 1 | 78 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 81 | 5 | 1 | 87 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001910.2 | 7 | MANE Select | |
| Ensembl | ENSP00000301729.4 | 7 | MANE Select | |
| RefSeq | NP_001171500.1 | 7 | Standard | |
| Ensembl | ENSP00000456319.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fatty acid degradation - Homo sapiens (human)
- Fatty Acid Beta Oxidation
- Mitochondrial LC-Fatty Acid Beta-Oxidation
- Liver steatosis AOP
- fatty acid &beta
Biological Process
- fatty acid beta-oxidation
Molecular Function
- dodecenoyl-CoA delta-isomerase activity
- enoyl-CoA hydratase activity
- intramolecular oxidoreductase activity
Cellular Component
- mitochondrion
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301729
- Coding exons
- 7
- Length
- 12906
- Individuals with no LoFs
- 125616
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 108
- Defined
- 125724
- p
- 0.000430
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.422 | 192 | 176 | 1.09 | 0.0000116 | 1891 |
| Missense (PolyPhen) | 66 | 62.556 | 1.055 | 640 | ||
| Synonymous | -0.571 | 91 | 84.3 | 1.08 | 0.00000620 | 657 |
| Loss of Function | -0.946 | 16 | 12.4 | 1.29 | 6.99e-7 | 133 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0020 | 0.0020 | notable |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00088 | 0.00071 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00030 | rare |
| South Asian | 0.00046 | 0.00046 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Able to isomerize both 3-cis and 3-trans double bonds into the 2-trans form in a range of enoyl-CoA species.;
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- RVIS EVS
- 0.06
- RVIS percentile EVS
- 58.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.786
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |