ECI2

protein-coding

enoyl-CoA delta isomerase 2

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, Aug 2011]

Previous symbols:

PECI

MANE transcript

NM_206836.3

Inheritance

—

ClinVar variants

P:1U:82B:10

Top phenotype

Familial hypercholesterolemia

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr6:4,115,693-4,135,597

External References & Databases

Ensembl (ENSG00000198721)

Transcript & Mutation Effects

hg38 • Region Span ~19.9 kb

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GenCC 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 ECI2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 3

Familial hypercholesterolemiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_206836.3. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			78 clinvar	7 clinvar	1 clinvar	86
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	82	8	2	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_206836.3	RefSeq	NP_996667.2	10	MANE Select
ENST00000380118.8	Ensembl	ENSP00000369461.3	10	MANE Select
NM_001166010.2	RefSeq	NP_001159482.1	9	Standard
NM_006117.3	RefSeq	NP_006108.2	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Peroxisome - Homo sapiens (human)
Fatty acid degradation - Homo sapiens (human)
fatty acid &beta
-oxidation (unsaturated, odd number)
Metabolism of lipids

Biological Process

protein targeting to peroxisome
fatty acid beta-oxidation using acyl-CoA oxidase

Molecular Function

fatty-acyl-CoA binding
dodecenoyl-CoA delta-isomerase activity
signaling receptor binding

Cellular Component

nucleoplasm
mitochondrion
peroxisome
peroxisomal matrix
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380118
Coding exons: 10
Length: 19909
Individuals with no LoFs: 125621
Homozygous LoFs: 0
Heterozygous LoFs: 127
Defined: 125748
p: 0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00850	215	215	1.00	0.0000106	2586
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0020	0.0020	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.0012	0.0011	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

RVIS EVS: 0.31
RVIS percentile EVS: 72.6

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	High
Cancer	High	Medium	High