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

    Gene ID: 55862, updated on 9-Dec-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. Predicted to be involved in fatty acid beta-oxidation. Predicted to be located in cytoplasm and membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in fat (RPKM 43.4), kidney (RPKM 24.8) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (127288712..127343609, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (128477670..128532553, complement)
    RS_2024_09 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. 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
    2. 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
    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 (48) 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)

    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_2024_08

    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

      UniProtKB/TrEMBL
      H0Y5L2

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

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

      UniProtKB/TrEMBL
      E9PPG7, J3KP84
      Related
      ENSP00000357272.2, ENST00000368289.6

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

      UniProtKB/TrEMBL
      E9PPG7, J3KP84

    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

      UniProtKB/TrEMBL
      H0Y5L2

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

      UniProtKB/TrEMBL
      H0Y5L2

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

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

      UniProtKB/TrEMBL
      E9PPG7, J3KP84

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

      UniProtKB/TrEMBL
      E9PPG7, J3KP84

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

      UniProtKB/TrEMBL
      F2Z2D6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NTX5.2 GenPept UniProtKB/Swiss-Prot:Q9NTX5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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