GeneBe

ECHS1

enoyl-CoA hydratase, short chain 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:133362485-133373354

Links

ENSG00000127884 ∙ NCBI:1892 ∙ OMIM:602292 ∙ HGNC:3151 ∙ Uniprot:P30084 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Strong), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Strong), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Strong), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Moderate), mode of inheritance: AR
  • Leigh syndrome with leukodystrophy (Supportive), mode of inheritance: AR
  • Leigh syndrome (Definitive), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Definitive), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Definitive), mode of inheritance: AR
  • mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Mitochondrial short-chain enoyl-CoA hydratase 1 deficiencyARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Neurologic25125611; 25393721; 26251176; 29575569

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ECHS1 gene.

  • not_provided (287 variants)
  • Mitochondrial_short-chain_Enoyl-Coa_hydratase_1_deficiency (74 variants)
  • Inborn_genetic_diseases (31 variants)
  • ECHS1-related_disorder (16 variants)
  • not_specified (12 variants)
  • Leigh_syndrome (3 variants)
  • See_cases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECHS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004092.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
73
clinvar
2
clinvar
 79
missense
10
clinvar
44
clinvar
92
clinvar
3
clinvar
 149
nonsense
1
clinvar
1
clinvar
1
clinvar
 3
start loss
3
2
 5
frameshift
6
clinvar
5
clinvar
2
clinvar
 13
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
3
clinvar
 7
Total 21 56 101 76 2

Highest pathogenic variant AF is 0.000256823

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ECHS1protein_codingprotein_codingENST00000368547 811210
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0008770.9431256820591257410.000235
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8631311620.8090.000009081867
Missense in Polyphen4174.020.55391823
Synonymous-0.4197065.71.070.00000429536
Loss of Function1.69713.80.5096.78e-7172

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007290.000727
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.0001400.000139
European (Non-Finnish)0.0002320.000229
Middle Eastern0.0001630.000163
South Asian0.0002960.000294
Other0.0003310.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Straight-chain enoyl-CoA thioesters from C4 up to at least C16 are processed, although with decreasing catalytic rate. Has high substrate specificity for crotonyl-CoA and moderate specificity for acryloyl-CoA, 3-methylcrotonyl-CoA and methacrylyl-CoA. It is noteworthy that binds tiglyl-CoA, but hydrates only a small amount of this substrate. {ECO:0000269|PubMed:26251176}.;
Pathway
Tryptophan metabolism - Homo sapiens (human);Butanoate metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Lysine degradation - Homo sapiens (human);Propanoate metabolism - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Long chain acyl-CoA dehydrogenase deficiency (LCAD);Lysine Degradation;3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Hyperlysinemia I, Familial;Malonyl-coa decarboxylase deficiency;2-aminoadipic 2-oxoadipic aciduria;Trifunctional protein deficiency;Long-chain-3-hydroxyacyl-coa dehydrogenase deficiency (LCHAD);Carnitine palmitoyl transferase deficiency (II);Very-long-chain acyl coa dehydrogenase deficiency (VLCAD);Medium chain acyl-coa dehydrogenase deficiency (MCAD);Malonic Aciduria;Fatty Acid Elongation In Mitochondria;Pyridoxine dependency with seizures;Saccharopinuria/Hyperlysinemia II;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Short Chain Acyl CoA Dehydrogenase Deficiency (SCAD Deficiency);Fatty acid Metabolism;Maple Syrup Urine Disease;Propanoate Metabolism;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Glutaric Aciduria Type I;Glutaric Aciduria Type I;Ethylmalonic Encephalopathy;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Mitochondrial Beta-Oxidation of Short Chain Saturated Fatty Acids;Mitochondrial Beta-Oxidation of Medium Chain Saturated Fatty Acids;Mitochondrial Beta-Oxidation of Long Chain Saturated Fatty Acids;Short-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (SCHAD);Methylmalonic Aciduria;Methylmalonic Aciduria Due to Cobalamin-Related Disorders;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Hyperlysinemia II or Saccharopinuria;Butyrate Metabolism;Beta-Ketothiolase Deficiency;Carnitine palmitoyl transferase deficiency (I);Fatty Acid Beta Oxidation;Fatty Acid Biosynthesis;Liver steatosis AOP;Tryptophan metabolism;Butanoate metabolism;Metabolism of lipids;Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA;Beta oxidation of octanoyl-CoA to hexanoyl-CoA;Beta oxidation of hexanoyl-CoA to butanoyl-CoA;Beta oxidation of butanoyl-CoA to acetyl-CoA;mitochondrial fatty acid beta-oxidation of saturated fatty acids;Mitochondrial Fatty Acid Beta-Oxidation;3-oxo-10R-octadecatrienoate beta-oxidation;Leukotriene metabolism;Saturated fatty acids beta-oxidation;Trihydroxycoprostanoyl-CoA beta-oxidation;Metabolism;Lysine degradation;Fatty acid metabolism;Propanoate metabolism;valine degradation;Mono-unsaturated fatty acid beta-oxidation;Omega-6 fatty acid metabolism;Valine, leucine and isoleucine degradation;Butanoate metabolism;Propanoate metabolism;Dimethyl-branched-chain fatty acid mitochondrial beta-oxidation;Di-unsaturated fatty acid beta-oxidation;Vitamin E metabolism;isoleucine degradation;fatty acid β-oxidation (peroxisome);fatty acid β-oxidation;glutaryl-CoA degradation;Tryptophan degradation;Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA;Valine Leucine Isoleucine degradation (Consensus)

Intolerance Scores

loftool
0.498
rvis_EVS
-0.07
rvis_percentile_EVS
48.35

Haploinsufficiency Scores

pHI
0.0927
hipred
Y
hipred_score
0.580
ghis
0.446

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.999

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Echs1
Phenotype

Gene ontology

Biological process
fatty acid beta-oxidation
Cellular component
mitochondrion;mitochondrial matrix
Molecular function
enoyl-CoA hydratase activity;protein binding