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    HACD4 3-hydroxyacyl-CoA dehydratase 4 [ Homo sapiens (human) ]

    Gene ID: 401494, updated on 9-Dec-2024

    Summary

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    Official Symbol
    HACD4provided by HGNC
    Official Full Name
    3-hydroxyacyl-CoA dehydratase 4provided by HGNC
    Primary source
    HGNC:HGNC:20920
    See related
    Ensembl:ENSG00000188921 MIM:615941; AllianceGenome:HGNC:20920
    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
    PTPLAD2
    Summary
    Enables enzyme binding activity and very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity. Involved in fatty acid elongation and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung (RPKM 8.9), bone marrow (RPKM 8.0) and 23 other tissues See more
    Orthologs
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    Genomic context

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    See HACD4 in Genome Data Viewer
    Location:
    9p21.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (20999509..21031640, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (21013385..21045517, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (20999508..21031639, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene focadhesin Neighboring gene microRNA 491 Neighboring gene small nucleolar RNA, H/ACA box 30B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:21031418-21031978 Neighboring gene uncharacterized LOC105375989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19805 Neighboring gene interferon nu 1, pseudogene

    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. The HACD4 haplotype as a risk factor for atherosclerosis in males. Zivotić I, et al. Gene, 2018 Jan 30. PMID 29031776
    2. PTPLAD2 is a tumor suppressor in esophageal squamous cell carcinogenesis. Zhu S, et al. FEBS Lett, 2014 Mar 18. PMID 24530685
    3. Inactivating Frameshift Mutations of HACD4 and TCP10L Tumor Suppressor Genes in Colorectal and Gastric Cancers. Jo YS, et al. Pathol Oncol Res, 2020 Jan. PMID 29532408
    4. Characterization of four mammalian 3-hydroxyacyl-CoA dehydratases involved in very long-chain fatty acid synthesis. Ikeda M, et al. FEBS Lett, 2008 Jul 9. PMID 18554506
    5. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. Cheng CY, et al. Am J Hum Genet, 2013 Aug 8. PMID 24144296, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686F01145, DKFZp686G24132

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3-hydroxyacyl-CoA dehydratase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables enzyme binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in fatty acid elongation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in fatty acid elongation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sphingolipid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in very long-chain fatty acid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in very long-chain fatty acid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4
    Names
    protein tyrosine phosphatase-like A domain containing 2
    protein tyrosine phosphatase-like protein PTPLAD2
    protein-tyrosine phosphatase-like A domain-containing protein 2
    very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase 4
    NP_001010915.2
    NP_001308812.1
    NP_001308832.1
    XP_016870202.1
    XP_047279346.1
    XP_054218939.1
    XP_054218940.1

    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_001010915.5 → NP_001010915.2  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform 1

      See identical proteins and their annotated locations for NP_001010915.2

      Status: VALIDATED

      Source sequence(s)
      AL662879, BC114215, BX648779, HY118500
      Consensus CDS
      CCDS43791.1
      UniProtKB/Swiss-Prot
      Q5VWC8, Q7Z385
      Related
      ENSP00000419503.1, ENST00000495827.3
      Conserved Domains (1) summary
      pfam04387
      Location:65 → 223
      PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

    2. NM_001321883.2 → NP_001308812.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL390882, AL662879, BC114215, BX538052, DA333010
      UniProtKB/Swiss-Prot
      Q5VWC8
      Conserved Domains (1) summary
      pfam04387
      Location:28 → 185
      PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

    3. NM_001321903.2 → NP_001308832.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL390882, AL662879
      Conserved Domains (1) summary
      pfam04387
      Location:65 → 273
      PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      20999509..21031640 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014713.2 → XP_016870202.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform X1

    2. XM_047423390.1 → XP_047279346.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      21013385..21045517 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362964.1 → XP_054218939.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform X1

    2. XM_054362965.1 → XP_054218940.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VWC8.1 GenPept UniProtKB/Swiss-Prot:Q5VWC8

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