Aliases for HACD4 Gene

Aliases for HACD4 Gene

  • 3-Hydroxyacyl-CoA Dehydratase 4 2 3 4 5
  • Very-Long-Chain (3R)-3-Hydroxyacyl-CoA Dehydratase 4 2 3 4
  • Protein-Tyrosine Phosphatase-Like A Domain-Containing Protein 2 3 4
  • Protein Tyrosine Phosphatase-Like A Domain Containing 2 2 3
  • PTPLAD2 3 4
  • Very-Long-Chain (3R)-3-Hydroxyacyl-[Acyl-Carrier Protein] Dehydratase 4 3
  • Protein Tyrosine Phosphatase-Like Protein PTPLAD2 3
  • OTTHUMG00000021016 2
  • Em:AL662879.1 2
  • EC 4.2.1.134 4
  • HACD4 5

External Ids for HACD4 Gene

Previous HGNC Symbols for HACD4 Gene

  • PTPLAD2

Summaries for HACD4 Gene

GeneCards Summary for HACD4 Gene

HACD4 (3-Hydroxyacyl-CoA Dehydratase 4) is a Protein Coding gene. Diseases associated with HACD4 include Spinocerebellar Ataxia 34. Among its related pathways are Metabolism and alpha-linolenic (omega3) and linoleic (omega6) acid metabolism. Gene Ontology (GO) annotations related to this gene include enzyme binding and 3-hydroxyacyl-CoA dehydratase activity. An important paralog of this gene is HACD3.

UniProtKB/Swiss-Prot Summary for HACD4 Gene

  • Catalyzes the third of the four reactions of the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process, allows the addition of two carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. This enzyme catalyzes the dehydration of the 3-hydroxyacyl-CoA intermediate into trans-2,3-enoyl-CoA, within each cycle of fatty acid elongation. Thereby, it participates in the production of VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators.

Additional gene information for HACD4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HACD4 Gene

Genomics for HACD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HACD4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J021030 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas 636.7 +0.6 569 2.2 BACH1 SMAD5 IKZF2 POLR2A ZNF341 PKNOX1 EED GATAD2B ZBTB40 ELF1 HACD4 LOC105375989 lnc-IFNB1-2 FOCAD
GH09J021016 Enhancer 0.9 FANTOM5 Ensembl ENCODE 30.2 +14.9 14911 4 TEAD4 CEBPB FOS MAFK USF2 SPI1 HACD4 IFNW1 IFNA1 IFNA6 FOCAD IFNA5 LOC105375989 lnc-IFNB1-2 piR-40176-033
GH09J020980 Enhancer 0.8 Ensembl ENCODE 28.1 +50.2 50212 2.6 IKZF2 EED RELB RUNX3 FOS BCL11A ARNT IKZF1 ZNF189 NR2F1 HACD4 piR-40176-033 LOC105375989 FOCAD
GH09J020997 Enhancer 0.7 Ensembl ENCODE 28.5 +34.7 34711 3.6 POLR2A IKZF2 PKNOX1 RUNX3 SPI1 IRF4 EBF1 ATF7 ETV6 CREM HACD4 piR-40176-033 LOC105375989 FOCAD
GH09J021094 Enhancer 0.9 FANTOM5 ENCODE 20.8 -64.3 -64285 3.1 IKZF2 SCRT2 CEBPB ARID3A DPF2 ZNF217 MAX EP300 IKZF1 GATA3 HACD4 FOCAD piR-61240-295 IFNWP4 IFNB1 IFNW1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HACD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HACD4

Genomic Locations for HACD4 Gene

Genomic Locations for HACD4 Gene
chr9:20,999,509-21,031,712
(GRCh38/hg38)
Size:
32,204 bases
Orientation:
Minus strand
chr9:20,995,306-21,031,635
(GRCh37/hg19)
Size:
36,330 bases
Orientation:
Minus strand

Genomic View for HACD4 Gene

Genes around HACD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HACD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HACD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HACD4 Gene

Proteins for HACD4 Gene

  • Protein details for HACD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VWC8-HACD4_HUMAN
    Recommended name:
    Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 4
    Protein Accession:
    Q5VWC8
    Secondary Accessions:
    • Q7Z385

    Protein attributes for HACD4 Gene

    Size:
    232 amino acids
    Molecular mass:
    27520 Da
    Quaternary structure:
    • May interact with enzymes of the ELO family (including ELOVL1); with those enzymes that mediate condensation, the first of the four steps of the reaction cycle responsible for fatty acids elongation, may be part of a larger fatty acids elongase complex.

neXtProt entry for HACD4 Gene

Post-translational modifications for HACD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HACD4 Gene

No data available for DME Specific Peptides for HACD4 Gene

Domains & Families for HACD4 Gene

Gene Families for HACD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for HACD4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HACD4 Gene

GenScript: Design optimal peptide antigens:
  • Protein-tyrosine phosphatase-like A domain-containing protein 2 (HACD4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5VWC8

UniProtKB/Swiss-Prot:

HACD4_HUMAN :
  • Belongs to the very long-chain fatty acids dehydratase HACD family.
Family:
  • Belongs to the very long-chain fatty acids dehydratase HACD family.
genes like me logo Genes that share domains with HACD4: view

Function for HACD4 Gene

Molecular function for HACD4 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the third of the four reactions of the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process, allows the addition of two carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. This enzyme catalyzes the dehydration of the 3-hydroxyacyl-CoA intermediate into trans-2,3-enoyl-CoA, within each cycle of fatty acid elongation. Thereby, it participates in the production of VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a very-long-chain (3R)-hydroxyacyl-CoA = a very-long-chain (2E)-enoyl-CoA + H2O; Xref=Rhea:RHEA:45812, ChEBI:CHEBI:15377, ChEBI:CHEBI:83728, ChEBI:CHEBI:85440; EC=4.2.1.134; Evidence={ECO:0000269|PubMed:18554506};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=6.8 uM for 3-hydroxypalmitoyl-CoA (at 37 degrees Celsius) {ECO:0000269|PubMed:18554506};

Enzyme Numbers (IUBMB) for HACD4 Gene

Phenotypes From GWAS Catalog for HACD4 Gene

Gene Ontology (GO) - Molecular Function for HACD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016829 lyase activity IEA --
GO:0018812 3-hydroxyacyl-CoA dehydratase activity IDA 18554506
GO:0019899 enzyme binding IDA 18554506
GO:0102158 very-long-chain 3-hydroxyacyl-CoA dehydratase activity IEA --
GO:0102343 3-hydroxy-arachidoyl-CoA dehydratase activity IEA --
genes like me logo Genes that share ontologies with HACD4: view

Animal Model Products

CRISPR Products

miRNA for HACD4 Gene

miRTarBase miRNAs that target HACD4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HACD4

No data available for Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HACD4 Gene

Localization for HACD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HACD4 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HACD4 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 2
mitochondrion 2
cytosol 2
extracellular 1
nucleus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for HACD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 18554506
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030176 integral component of endoplasmic reticulum membrane IBA 21873635
genes like me logo Genes that share ontologies with HACD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HACD4 Gene

Pathways & Interactions for HACD4 Gene

genes like me logo Genes that share pathways with HACD4: view

UniProtKB/Swiss-Prot Q5VWC8-HACD4_HUMAN

  • Pathway: Lipid metabolism; fatty acid biosynthesis.

Interacting Proteins for HACD4 Gene

Gene Ontology (GO) - Biological Process for HACD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006631 fatty acid metabolic process IEA --
GO:0006633 fatty acid biosynthetic process IEA --
GO:0030148 sphingolipid biosynthetic process IBA 21873635
GO:0030497 fatty acid elongation IDA 18554506
genes like me logo Genes that share ontologies with HACD4: view

No data available for SIGNOR curated interactions for HACD4 Gene

Drugs & Compounds for HACD4 Gene

(1) Drugs for HACD4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with HACD4: view

Transcripts for HACD4 Gene

mRNA/cDNA for HACD4 Gene

3 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HACD4

Alternative Splicing Database (ASD) splice patterns (SP) for HACD4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8
SP1: - - -
SP2:

Relevant External Links for HACD4 Gene

GeneLoc Exon Structure for
HACD4

Expression for HACD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HACD4 Gene

Protein differential expression in normal tissues from HIPED for HACD4 Gene

This gene is overexpressed in Platelet (47.3), Placenta (11.5), and CD4 Tcells (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HACD4 Gene



Protein tissue co-expression partners for HACD4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HACD4

mRNA Expression by UniProt/SwissProt for HACD4 Gene:

Q5VWC8-HACD4_HUMAN
Tissue specificity: Highly expressed in leukocytes, and low expression in heart, spleen, kidney, and placenta.

Evidence on tissue expression from TISSUES for HACD4 Gene

  • Intestine(4.3)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with HACD4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HACD4 Gene

Orthologs for HACD4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HACD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTPLAD2 30 31
  • 99.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PTPLAD2 30 31
  • 91.74 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTPLAD2 30 31
  • 91.41 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PTPLAD2 31
  • 87 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptplad2 30
  • 86.93 (n)
Mouse
(Mus musculus)
Mammalia Ptplad2 30 31
  • 85.34 (n)
OneToOne
Hacd4 17
Platypus
(Ornithorhynchus anatinus)
Mammalia PTPLAD2 31
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LOC100857583 30
  • 70.85 (n)
-- 31
  • 59 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia PTPLAD2 31
  • 60 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100490902 30
  • 64.08 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC561303 30
  • 56.65 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG9267 31
  • 19 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHS1 31
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3155 31
  • 15 (a)
OneToMany
Species where no ortholog for HACD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for HACD4 Gene

ENSEMBL:
Gene Tree for HACD4 (if available)
TreeFam:
Gene Tree for HACD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HACD4: view image

Paralogs for HACD4 Gene

Paralogs for HACD4 Gene

genes like me logo Genes that share paralogs with HACD4: view

Variants for HACD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HACD4 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs2298260 - p.Thr36Ala

Additional dbSNP identifiers (rs#s) for HACD4 Gene

Structural Variations from Database of Genomic Variants (DGV) for HACD4 Gene

Variant ID Type Subtype PubMed ID
esv2764150 CNV gain+loss 21179565
nsv1017312 CNV gain 25217958
nsv1161847 CNV deletion 26073780
nsv613752 CNV loss 21841781

Variation tolerance for HACD4 Gene

Residual Variation Intolerance Score: 54.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.75; 86.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HACD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HACD4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HACD4 Gene

Disorders for HACD4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HACD4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spinocerebellar ataxia 34
  • sca34
- elite association - COSMIC cancer census association via MalaCards
Search HACD4 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with HACD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HACD4 Gene

Publications for HACD4 Gene

  1. Characterization of four mammalian 3-hydroxyacyl-CoA dehydratases involved in very long-chain fatty acid synthesis. (PMID: 18554506) Ikeda M … Kihara A (FEBS letters 2008) 2 3 4
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. The HACD4 haplotype as a risk factor for atherosclerosis in males. (PMID: 29031776) Zivotić I … Zivković M (Gene 2018) 3
  4. PTPLAD2 is a tumor suppressor in esophageal squamous cell carcinogenesis. (PMID: 24530685) Zhu S … Zhang W (FEBS letters 2014) 3
  5. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. (PMID: 24144296) Cheng CY … Baird PN (American journal of human genetics 2013) 3

Products for HACD4 Gene

Sources for HACD4 Gene