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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			30	1	1	32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	1

Variants in ECI1

This is a list of pathogenic ClinVar variants found in the ECI1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-2239989-T-C		not specified	Uncertain significance (Sep 16, 2021)
16-2240015-C-A		not specified	Uncertain significance (Dec 14, 2023)
16-2240037-T-A		not specified	Uncertain significance (Jun 06, 2023)
16-2240068-C-T		not specified	Uncertain significance (Jan 11, 2023)
16-2240070-T-C		not specified	Uncertain significance (Jul 13, 2022)
16-2240079-C-T		not specified	Uncertain significance (Mar 14, 2023)
16-2240094-C-T		not specified	Uncertain significance (Aug 11, 2022)
16-2240095-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-2240103-G-A			Uncertain significance (Jan 01, 2018)
16-2240112-C-T		not specified	Uncertain significance (May 22, 2023)
16-2243069-A-G		not specified	Uncertain significance (Jun 24, 2022)
16-2243147-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-2243166-G-T		not specified	Uncertain significance (Mar 13, 2023)
16-2243196-C-T		not specified	Uncertain significance (May 08, 2024)
16-2243199-T-A		not specified	Uncertain significance (Dec 01, 2022)
16-2243208-C-T		not specified	Uncertain significance (Feb 13, 2015)
16-2243391-G-C		not specified	Uncertain significance (May 14, 2024)
16-2244431-T-A		not specified	Uncertain significance (Nov 17, 2022)
16-2244447-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-2244465-C-T		not specified	Uncertain significance (Dec 27, 2022)
16-2244469-C-A		not specified	Uncertain significance (Oct 02, 2023)
16-2244486-A-G		not specified	Uncertain significance (Aug 10, 2021)
16-2244492-C-T		not specified	Uncertain significance (Jun 11, 2021)
16-2244513-C-T		not specified	Uncertain significance (Dec 02, 2022)
16-2244515-G-A		not specified	Uncertain significance (Oct 06, 2022)

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
1.59e-12	0.00788	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

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.177
• ghis: 0.442

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

Mouse Genome Informatics

• Gene name: Eci1
• Phenotype: renal/urinary system phenotype; homeostasis/metabolism phenotype

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