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ECHDC1 ethylmalonyl-CoA decarboxylase 1 [ Homo sapiens (human) ]

Gene ID: 55862, updated on 3-Apr-2024

Summary

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Official Symbol
ECHDC1provided by HGNC
Official Full Name
ethylmalonyl-CoA decarboxylase 1provided by HGNC
Primary source
HGNC:HGNC:21489
See related
Ensembl:ENSG00000093144 MIM:612136; AllianceGenome:HGNC:21489
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MMCD; HEL-S-76; dJ351K20.2
Summary
Predicted to enable carboxy-lyase activity and enoyl-CoA hydratase activity. Predicted to be involved in fatty acid beta-oxidation. Predicted to be integral component of membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 43.4), kidney (RPKM 24.8) and 25 other tissues See more
Orthologs
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Genomic context

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See ECHDC1 in Genome Data Viewer
Location:
6q22.33
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (127288712..127343609, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (128477670..128532553, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (127609857..127664754, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25039 Neighboring gene ring finger protein 146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17528 Neighboring gene uncharacterized LOC105377994 Neighboring gene RNA, 5S ribosomal pseudogene 217 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:127653558-127654108 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:127654109-127654658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:127664039-127664912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:127665787-127666660 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta pseudogene 4 Neighboring gene ribosomal protein L5 pseudogene 18

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Variants in the ethylmalonyl-CoA decarboxylase (ECHDC1) gene: a novel player in ethylmalonic aciduria? Fogh S, et al. J Inherit Metab Dis, 2021 Sep. PMID 33973257, Free PMC Article
  2. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Jaiswal A, et al. Mol Syst Biol, 2021 Mar. PMID 33750001, Free PMC Article
  3. Risk of breast and prostate cancer is not associated with increased homozygosity in outbred populations. Enciso-Mora V, et al. Eur J Hum Genet, 2010 Aug. PMID 20407466, Free PMC Article
  4. The RNF146 and ECHDC1 genes as candidates for inherited breast and ovarian cancer in Jewish Ashkenazi women. Menachem TD, et al. Fam Cancer, 2009. PMID 19517271
  5. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Gold B, et al. Proc Natl Acad Sci U S A, 2008 Mar 18. PMID 18326623, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Variants in the ethylmalonyl-CoA decarboxylase (ECHDC1) gene: a novel player in ethylmalonic aciduria?
    Title: Variants in the ethylmalonyl-CoA decarboxylase (ECHDC1) gene: a novel player in ethylmalonic aciduria?
  2. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.
    Title: Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.
  3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Risk of breast and prostate cancer is not associated with increased homozygosity in outbred populations.
  4. Mutations in the coding regions of the RNF146 and ECHDC1 genes do not contribute to the burden of inherited predisposition of breast cancer in Ashkenazi high risk women.
    Title: The RNF146 and ECHDC1 genes as candidates for inherited breast and ovarian cancer in Jewish Ashkenazi women.
  5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Evaluation of 11 breast cancer susceptibility loci in African-American women.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: The RNF146 and ECHDC1 genes as candidates for inherited breast and ovarian cancer in Jewish Ashkenazi women.
  7. Genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ40827, DKFZp762M1110

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carboxy-lyase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables methyl/ethyl malonyl-CoA decarboxylase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in fatty acid beta-oxidation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
ethylmalonyl-CoA decarboxylase
Names
enoyl CoA hydratase domain containing 1
enoyl Coenzyme A hydratase domain containing 1
enoyl-CoA hydratase domain-containing protein 1
epididymis secretory protein Li 76
methylmalonyl-CoA decarboxylase
NP_001002030.1
NP_001099014.1
NP_001099015.1
NP_001132982.1
NP_060949.2
XP_005267104.1
XP_011534245.1
XP_047275027.1
XP_047275028.1
XP_047275029.1
XP_047275030.1
XP_054211896.1
XP_054211897.1
XP_054211898.1
XP_054211899.1
XP_054211900.1
XP_054211901.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001002030.2 → NP_001002030.1  ethylmalonyl-CoA decarboxylase isoform 1

    See identical proteins and their annotated locations for NP_001002030.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AL834469, DC297239
    Consensus CDS
    CCDS43504.1
    UniProtKB/TrEMBL
    H0Y5L2
    Related
    ENSP00000401751.3, ENST00000454859.8
    Conserved Domains (1) summary
    cd06558
    Location:54 → 245
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  2. NM_001105544.2 → NP_001099014.1  ethylmalonyl-CoA decarboxylase isoform 3

    See identical proteins and their annotated locations for NP_001099014.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1, which causes a downstream AUG start codon to be used. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL834469, BE896631, DC297239
    Consensus CDS
    CCDS47472.1
    UniProtKB/Swiss-Prot
    Q9NTX5
    Related
    ENSP00000404866.2, ENST00000454591.6
    Conserved Domains (1) summary
    cd06558
    Location:1 → 170
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  3. NM_001105545.2 → NP_001099015.1  ethylmalonyl-CoA decarboxylase isoform 4

    See identical proteins and their annotated locations for NP_001099015.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two alternate exons compared to variant 1, which causes a frameshift and a downstream AUG start codon to be used. The resulting isoform (4) has a distinct C-terminus and is shorter at both the N- and C-termini compared to isoform 1.
    Source sequence(s)
    AL834469, DA846978, DC297239
    Consensus CDS
    CCDS55054.1
    UniProtKB/Swiss-Prot
    Q9NTX5
    Related
    ENSP00000436109.1, ENST00000528402.5
    Conserved Domains (1) summary
    cl23717
    Location:1 → 49
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  4. NM_001139510.2 → NP_001132982.1  ethylmalonyl-CoA decarboxylase isoform 5

    See identical proteins and their annotated locations for NP_001132982.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate 5' exon, thus differing in its 5' UTR and 5' coding region, compared to variant 1. The resulting isoform (5) is longer at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK025760, AK025796, AL834469, BU684175
    Consensus CDS
    CCDS47471.1
    UniProtKB/Swiss-Prot
    A6NFJ5, B7Z8S0, E9PEN7, E9PR31, F8W851, Q5TEF6, Q5TEF7, Q5TEG0, Q5TEG4, Q9NTX5, Q9NZ30, V9HW18
    UniProtKB/TrEMBL
    H0Y5L2
    Related
    ENSP00000436585.1, ENST00000531967.5
    Conserved Domains (1) summary
    cd06558
    Location:60 → 251
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  5. NM_018479.4 → NP_060949.2  ethylmalonyl-CoA decarboxylase isoform 2

    See identical proteins and their annotated locations for NP_060949.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL834469, BQ224769, DC297239
    Consensus CDS
    CCDS34530.1
    UniProtKB/TrEMBL
    E9PPG7, J3KP84
    Related
    ENSP00000357274.2, ENST00000368291.6
    Conserved Domains (1) summary
    cd06558
    Location:54 → 124
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    127288712..127343609 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005267047.4 → XP_005267104.1  ethylmalonyl-CoA decarboxylase isoform X1

    See identical proteins and their annotated locations for XP_005267104.1

    UniProtKB/TrEMBL
    H0Y5L2
    Related
    ENSP00000402492.2, ENST00000430841.6
    Conserved Domains (1) summary
    cd06558
    Location:54 → 245
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  2. XM_047419071.1 → XP_047275027.1  ethylmalonyl-CoA decarboxylase isoform X1

  3. XM_047419074.1 → XP_047275030.1  ethylmalonyl-CoA decarboxylase isoform X5

  4. XM_047419073.1 → XP_047275029.1  ethylmalonyl-CoA decarboxylase isoform X3

    Related
    ENSP00000357272.2, ENST00000368289.6

  5. XM_047419072.1 → XP_047275028.1  ethylmalonyl-CoA decarboxylase isoform X2

  6. XM_011535943.3 → XP_011534245.1  ethylmalonyl-CoA decarboxylase isoform X4

    UniProtKB/TrEMBL
    F2Z2D6
    Related
    ENSP00000436703.1, ENST00000368292.10
    Conserved Domains (1) summary
    cd06558
    Location:60 → 145
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    128477670..128532553 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355921.1 → XP_054211896.1  ethylmalonyl-CoA decarboxylase isoform X1

  2. XM_054355922.1 → XP_054211897.1  ethylmalonyl-CoA decarboxylase isoform X1

  3. XM_054355926.1 → XP_054211901.1  ethylmalonyl-CoA decarboxylase isoform X5

  4. XM_054355924.1 → XP_054211899.1  ethylmalonyl-CoA decarboxylase isoform X3

  5. XM_054355923.1 → XP_054211898.1  ethylmalonyl-CoA decarboxylase isoform X2

  6. XM_054355925.1 → XP_054211900.1  ethylmalonyl-CoA decarboxylase isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NTX5.2 GenPept UniProtKB/Swiss-Prot:Q9NTX5

Gene LinkOut

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