ECI1

enoyl-CoA delta isomerase 1

Basic information

Region (hg38): 16:2239402-2252300

Previous symbols: [ "DCI" ]

Links

ENSG00000167969 ∙ NCBI:1632 ∙ OMIM:600305 ∙ HGNC:2703 ∙ Uniprot:P42126 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 12.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001919.4	NP_001910.2	7	yes	-
ENST00000301729.9	ENSP00000301729.4	7	yes	-
NM_001178029.2	NP_001171500.1	7	-	-
ENST00000562238.5	ENSP00000456319.1	7	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ECI1 gene.

• not_specified (73 variants)
• not_provided (6 variants)
• Complex_I_deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECI1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001919.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	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

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECI1	protein_coding	protein_coding	ENST00000301729	7	12906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125616	0	108	125724	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.422	192	176	1.09	0.0000116	1891
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00233	0.00232
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000879	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000321	0.000299
Middle Eastern	0.000879	0.000707
South Asian	0.000460	0.000457
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Fatty acid degradation - Homo sapiens (human);Fatty Acid Beta Oxidation;Mitochondrial LC-Fatty Acid Beta-Oxidation;Liver steatosis AOP;fatty acid β-oxidation (unsaturated, odd number);Metabolism of lipids;mitochondrial fatty acid beta-oxidation of unsaturated fatty acids;Mitochondrial Fatty Acid Beta-Oxidation;Metabolism;Fatty acid metabolism;Omega-6 fatty acid metabolism;Di-unsaturated fatty acid beta-oxidation;fatty acid β-oxidation (Consensus)

Recessive Scores

• pRec: 0.239

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.786

Gene Damage Prediction

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

Gene ontology

• Biological process: fatty acid beta-oxidation
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: dodecenoyl-CoA delta-isomerase activity;enoyl-CoA hydratase activity;intramolecular oxidoreductase activity