ECH1

enoyl-CoA hydratase 1

Basic information

Region (hg38): 19:38815422-38831841

Links

ENSG00000104823 ∙ NCBI:1891 ∙ OMIM:600696 ∙ HGNC:3149 ∙ Uniprot:Q13011 ∙ 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 ECH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECH1 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			32		3	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	32	0	5

Variants in ECH1

This is a list of pathogenic ClinVar variants found in the ECH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38815619-C-G		not specified	Uncertain significance (Nov 23, 2024)
19-38815623-G-A		not specified	Uncertain significance (Oct 04, 2022)
19-38815684-C-T		not specified	Uncertain significance (Apr 22, 2024)
19-38815713-G-A		not specified	Uncertain significance (Aug 10, 2023)
19-38815889-C-T			Benign (-)
19-38815960-A-G		not specified	Uncertain significance (Aug 17, 2022)
19-38815964-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-38816003-C-T		not specified	Uncertain significance (Jun 07, 2024)
19-38816299-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-38816305-G-A		not specified	Uncertain significance (May 02, 2024)
19-38816319-C-G		not specified	Uncertain significance (Feb 28, 2023)
19-38816327-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-38816463-C-T			Benign (-)
19-38816469-C-A		not specified	Uncertain significance (Jul 05, 2024)
19-38816480-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-38817099-C-T		not specified	Uncertain significance (Jan 16, 2025)
19-38817456-C-T		not specified	Uncertain significance (Mar 08, 2024)
19-38817462-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-38817492-T-A		not specified	Uncertain significance (Sep 01, 2021)
19-38817505-C-G		not specified	Uncertain significance (Aug 12, 2021)
19-38817533-T-C		not specified	Uncertain significance (Aug 04, 2023)
19-38817550-C-T			Benign (-)
19-38817575-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-38831051-G-C			Benign (Feb 14, 2018)
19-38831069-G-C			Uncertain significance (Jan 04, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECH1	protein_coding	protein_coding	ENST00000221418	10	16584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.16e-7	0.694	125639	1	108	125748	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0436	205	207	0.991	0.0000120	2115
Missense in Polyphen		75	84.48	0.88779		861
Synonymous	0.786	82	91.6	0.895	0.00000626	664
Loss of Function	1.16	12	17.2	0.698	8.06e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000846	0.000846
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000389	0.000387
Middle Eastern	0.000761	0.000761
South Asian	0.000425	0.000425
Other	0.000980	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isomerization of 3-trans,5-cis-dienoyl-CoA to 2-trans,4- trans-dienoyl-CoA. {ECO:0000250}.
• Pathway: Peroxisome - Homo sapiens (human);Valproic Acid Pathway, Pharmacokinetics;Fatty Acid Biosynthesis;Liver steatosis AOP;Metabolism of proteins;Peroxisomal protein import;Omega-6 fatty acid metabolism (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.745
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.172
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ech1

Gene ontology

• Biological process: protein targeting to peroxisome;fatty acid beta-oxidation
• Cellular component: mitochondrion;peroxisome;peroxisomal matrix;cytosol;membrane;extracellular exosome
• Molecular function: signaling receptor binding;protein binding;delta3,5-delta2,4-dienoyl-CoA isomerase activity