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

Gene ID: 401494, updated on 11-Apr-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 3-hydroxyacyl-CoA dehydratase activity and enzyme binding activity. Involved in fatty acid elongation and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
9p21.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (20999509..21031640, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (21013385..21045517, complement)
105.20220307 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)

Genotypes

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
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
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_2023_10

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

Gene LinkOut

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