ECI2

enoyl-CoA delta isomerase 2

Basic information

Region (hg38): 6:4115693-4135597

Previous symbols: [ "PECI" ]

Links

ENSG00000198721 ∙ NCBI:10455 ∙ OMIM:608024 ∙ HGNC:14601 ∙ Uniprot:O75521 ∙ 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 ECI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECI2 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					1	1
missense			23	2	1	26
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	3	2

Variants in ECI2

This is a list of pathogenic ClinVar variants found in the ECI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-4115909-C-T		not specified	Uncertain significance (Dec 12, 2023)
6-4117312-G-T		not specified	Uncertain significance (Feb 13, 2024)
6-4117360-A-G		not specified	Uncertain significance (Sep 25, 2023)
6-4117373-G-A			Benign (Aug 15, 2017)
6-4117414-G-T		not specified	Uncertain significance (May 29, 2024)
6-4117442-T-C		not specified	Uncertain significance (May 26, 2024)
6-4119187-T-G		not specified	Uncertain significance (Mar 24, 2023)
6-4119205-T-C		not specified	Uncertain significance (Mar 28, 2024)
6-4125260-G-A		not specified	Uncertain significance (Aug 08, 2023)
6-4125267-C-T		not specified	Uncertain significance (Mar 14, 2023)
6-4125299-A-G		not specified	Uncertain significance (Jan 26, 2022)
6-4125353-A-G		not specified	Uncertain significance (Dec 13, 2023)
6-4126146-G-A			Benign (Aug 15, 2017)
6-4126148-C-T		not specified	Uncertain significance (May 04, 2022)
6-4126184-G-T		not specified	Uncertain significance (Feb 05, 2024)
6-4126192-G-A		not specified	Uncertain significance (Nov 12, 2021)
6-4126229-C-T		not specified	Uncertain significance (Dec 21, 2022)
6-4130383-T-C		not specified	Uncertain significance (Jun 01, 2022)
6-4130425-T-C		not specified	Uncertain significance (Oct 12, 2021)
6-4130464-T-C		not specified	Uncertain significance (Jan 20, 2023)
6-4130541-T-C		not specified	Uncertain significance (Mar 20, 2023)
6-4130542-A-G		not specified	Uncertain significance (Aug 30, 2022)
6-4130796-C-T		not specified	Uncertain significance (Aug 02, 2023)
6-4133559-A-G		not specified	Uncertain significance (Apr 06, 2022)
6-4133563-C-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECI2	protein_coding	protein_coding	ENST00000380118	10	19909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.55e-8	0.453	125621	0	127	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00850	215	215	1.00	0.0000106	2586
Missense in Polyphen		65	75.967	0.85564		880
Synonymous	1.14	69	82.2	0.839	0.00000456	751
Loss of Function	0.851	13	16.8	0.776	7.04e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00196	0.00196
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00196	0.00196
South Asian	0.00115	0.00114
Other	0.000163	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. Has a preference for 3-trans substrates (By similarity). {ECO:0000250}.
• Pathway: Peroxisome - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);fatty acid β-oxidation (unsaturated, odd number);Metabolism of lipids;Metabolism of proteins;Leukotriene metabolism;Beta-oxidation of very long chain fatty acids;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism;Omega-6 fatty acid metabolism;Di-unsaturated fatty acid beta-oxidation;fatty acid β-oxidation (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0829
• hipred: N
• hipred_score: 0.187
• ghis: 0.457

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	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Eci2

Gene ontology

• Biological process: protein targeting to peroxisome;fatty acid beta-oxidation using acyl-CoA oxidase
• Cellular component: nucleoplasm;mitochondrion;peroxisome;peroxisomal matrix;cytosol;membrane;intracellular membrane-bounded organelle
• Molecular function: fatty-acyl-CoA binding;dodecenoyl-CoA delta-isomerase activity;signaling receptor binding