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Aliases for HACD2 Gene

Aliases for HACD2 Gene

  • 3-Hydroxyacyl-CoA Dehydratase 2 2 3 4 5
  • Protein Tyrosine Phosphatase-Like (Proline Instead Of Catalytic Arginine), Member B 2 3
  • Very-Long-Chain (3R)-3-Hydroxyacyl-CoA Dehydratase 2 2 3
  • Protein-Tyrosine Phosphatase-Like Member B 3 4
  • PTPLB 3 4
  • Very-Long-Chain (3R)-3-Hydroxyacyl-[Acyl-Carrier Protein] Dehydratase 2 3
  • EC 4.2.1.134 4

External Ids for HACD2 Gene

Previous HGNC Symbols for HACD2 Gene

  • PTPLB

Summaries for HACD2 Gene

Entrez Gene Summary for HACD2 Gene

  • The protein encoded by this gene can catalyze the third step (dehydration) in the conversion of long chain fatty acids to very long chain fatty acids. The encoded protein localizes to the endoplasmic reticulum membrane. [provided by RefSeq, Jul 2016]

GeneCards Summary for HACD2 Gene

HACD2 (3-Hydroxyacyl-CoA Dehydratase 2) is a Protein Coding gene. Among its related pathways are Fatty Acyl-CoA Biosynthesis and Metabolism. Gene Ontology (GO) annotations related to this gene include enzyme binding and lyase activity. An important paralog of this gene is HACD1.

UniProtKB/Swiss-Prot for HACD2 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 HACD2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HACD2 Gene

Genomics for HACD2 Gene

GeneHancer (GH) Regulatory Elements for HACD2 Gene

Promoters and enhancers for HACD2 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
GH03J123581 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE 658.8 -0.1 -77 6.5 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 HACD2 MYLK-AS1 ADCY5 GC03P123375
GH03J123617 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 18.6 -34.9 -34853 5.1 CLOCK FOXA2 NFIB NEUROD1 SIN3A RFX5 HSF1 ZSCAN5C SCRT2 RCOR1 MYLK HACD2 MYLK-AS1 GC03M123611 PIR59914
GH03J123631 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 21.2 -47.5 -47454 1.9 USF1 FOXA2 RXRA SIN3A EP300 ZIC2 NR2F2 SP1 JUND ATF3 PIR59914 HACD2 MYLK-AS1 ADCY5 MYLK-AS2 MYLK
GH03J123652 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.8 -68.3 -68344 2.3 ELF3 PKNOX1 ZSCAN4 ARID4B DMAP1 ZNF48 RAD21 YY1 ZNF614 HSF1 MYLK MYLK-AS2 HACD2 MYLK-AS1 ROPN1 PIR59914
GH03J123636 Enhancer 0.9 ENCODE dbSUPER 17.7 -51.9 -51919 2.1 NCOA3 MEIS2 PKNOX1 TEAD4 TAL1 NEUROD1 SIN3A TCF12 CTBP1 NCOR1 HACD2 MYLK-AS2 MYLK MYLK-AS1 ROPN1 PIR59914
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HACD2 on UCSC Golden Path with GeneCards custom track

Genomic Locations for HACD2 Gene

Genomic Locations for HACD2 Gene
chr3:123,490,820-123,585,185
(GRCh38/hg38)
Size:
94,366 bases
Orientation:
Minus strand
chr3:123,209,667-123,304,032
(GRCh37/hg19)
Size:
94,366 bases
Orientation:
Minus strand

Genomic View for HACD2 Gene

Genes around HACD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HACD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HACD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HACD2 Gene

Proteins for HACD2 Gene

  • Protein details for HACD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6Y1H2-HACD2_HUMAN
    Recommended name:
    Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2
    Protein Accession:
    Q6Y1H2

    Protein attributes for HACD2 Gene

    Size:
    254 amino acids
    Molecular mass:
    28368 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 (PubMed:18554506). Interacts with BCAP31 (PubMed:15024066).
    Miscellaneous:
    • Turns over rapidly through degradation by the proteasome system.

neXtProt entry for HACD2 Gene

Post-translational modifications for HACD2 Gene

  • Glycosylation at isoforms=209
  • Ubiquitination at Lys11
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HACD2 Gene

Domains & Families for HACD2 Gene

Gene Families for HACD2 Gene

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

Protein Domains for HACD2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HACD2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6Y1H2

UniProtKB/Swiss-Prot:

HACD2_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 HACD2: view

Function for HACD2 Gene

Molecular function for HACD2 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:
A very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain trans-2,3-dehydroacyl-CoA + H(2)O.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=121.7 uM for 3-hydroxypalmitoyl-CoA (at 37 degrees Celsius) {ECO:0000269 PubMed:18554506};

Enzyme Numbers (IUBMB) for HACD2 Gene

Phenotypes From GWAS Catalog for HACD2 Gene

Gene Ontology (GO) - Molecular Function for HACD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004725 NOT protein tyrosine phosphatase activity IMP 15024066
GO:0005515 protein binding IPI 15024066
GO:0016829 lyase activity IEA --
GO:0018812 3-hydroxyacyl-CoA dehydratase activity IDA 18554506
GO:0019899 enzyme binding IDA 18554506
genes like me logo Genes that share ontologies with HACD2: view
genes like me logo Genes that share phenotypes with HACD2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for HACD2

CRISPR Products

miRNA for HACD2 Gene

miRTarBase miRNAs that target HACD2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HACD2

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HACD2 Gene

Localization for HACD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HACD2 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 HACD2 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HACD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 15024066
GO:0005789 endoplasmic reticulum membrane IEA,TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030176 integral component of endoplasmic reticulum membrane IBA --
genes like me logo Genes that share ontologies with HACD2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HACD2 Gene

Pathways & Interactions for HACD2 Gene

genes like me logo Genes that share pathways with HACD2: view

UniProtKB/Swiss-Prot Q6Y1H2-HACD2_HUMAN

  • Pathway: Lipid metabolism; fatty acid biosynthesis.

Gene Ontology (GO) - Biological Process for HACD2 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 IGI 18554506
GO:0030497 fatty acid elongation IDA 18554506
genes like me logo Genes that share ontologies with HACD2: view

No data available for SIGNOR curated interactions for HACD2 Gene

Drugs & Compounds for HACD2 Gene

(1) Drugs for HACD2 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 HACD2: view

Transcripts for HACD2 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HACD2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HACD2 Gene

No ASD Table

Relevant External Links for HACD2 Gene

GeneLoc Exon Structure for
HACD2
ECgene alternative splicing isoforms for
HACD2

Expression for HACD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HACD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HACD2 Gene

This gene is overexpressed in Nasal epithelium (44.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HACD2 Gene



Protein tissue co-expression partners for HACD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of HACD2 Gene:

HACD2

mRNA Expression by UniProt/SwissProt for HACD2 Gene:

Q6Y1H2-HACD2_HUMAN
Tissue specificity: Highly expressed in testis, spleen, prostate, colon and heart, followed by moderate expression in thymus, ovary, small intestine, peripheral blood leukocytes, liver, skeletal muscle and pancreas. Weakly detected in kidney, placenta, brain and lung.

Evidence on tissue expression from TISSUES for HACD2 Gene

  • Nervous system(4.6)
  • Liver(4.4)
genes like me logo Genes that share expression patterns with HACD2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HACD2 Gene

Orthologs for HACD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HACD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PTPLB 34 33
  • 99.48 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PTPLB 34 33
  • 95.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PTPLB 34 33
  • 93.6 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ptplb 34 33
  • 90.75 (n)
OneToOne
Hacd2 16
rat
(Rattus norvegicus)
Mammalia Ptplb 33
  • 89.04 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 79 (a)
OneToMany
-- 34
  • 52 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia PTPLB 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves PTPLB 34 33
  • 81.27 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PTPLB 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ptplb 33
  • 73.81 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4083 33
zebrafish
(Danio rerio)
Actinopterygii ptplb 34 33
  • 76.25 (n)
OneToOne
wufi32c08 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12011 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003814 33
  • 50.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6746 34 33
  • 49.77 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hpo-8 34 33
  • 51.26 (n)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR090W 33
  • 47.7 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHS1 34
  • 34 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons PAS2 33
  • 48.17 (n)
rice
(Oryza sativa)
Liliopsida Os01g0150200 33
  • 48.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.263 34
  • 52 (a)
OneToMany
Cin.2432 33
bread mold
(Neurospora crassa)
Ascomycetes NCU08985 33
  • 47.48 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2432 33
Species where no ortholog for HACD2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HACD2 Gene

ENSEMBL:
Gene Tree for HACD2 (if available)
TreeFam:
Gene Tree for HACD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HACD2: view image

Paralogs for HACD2 Gene

Paralogs for HACD2 Gene

genes like me logo Genes that share paralogs with HACD2: view

Variants for HACD2 Gene

Sequence variations from dbSNP and Humsavar for HACD2 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000005395 -- 123,585,141(-) C/T upstream_transcript_variant
rs1000052780 -- 123,537,613(-) T/G intron_variant
rs1000067830 -- 123,522,522(-) T/C intron_variant
rs1000074844 -- 123,569,974(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000103216 -- 123,537,365(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HACD2 Gene

Variant ID Type Subtype PubMed ID
dgv2586n106 CNV deletion 24896259
esv1612025 CNV deletion 17803354
esv1714874 CNV insertion 17803354
esv2305385 CNV deletion 18987734
esv2584472 CNV deletion 19546169
esv2725841 CNV deletion 23290073
esv2834236 CNV deletion 24192839
esv3562483 CNV deletion 23714750
esv3597626 CNV gain 21293372
esv5391 CNV loss 18987735
esv9393 CNV loss 19470904
esv992794 CNV deletion 20482838
nsv1073673 CNV deletion 25765185
nsv3978 CNV deletion 18451855
nsv477197 CNV novel sequence insertion 20440878
nsv507122 OTHER sequence alteration 20534489
nsv829707 CNV loss 17160897
nsv829708 CNV gain 17160897
nsv829709 CNV loss 17160897
nsv956811 CNV deletion 24416366

Variation tolerance for HACD2 Gene

Residual Variation Intolerance Score: 63.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.09; 2.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HACD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HACD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HACD2 Gene

Disorders for HACD2 Gene

Additional Disease Information for HACD2

No disorders were found for HACD2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HACD2 Gene

Publications for HACD2 Gene

  1. The yeast split-ubiquitin membrane protein two-hybrid screen identifies BAP31 as a regulator of the turnover of endoplasmic reticulum-associated protein tyrosine phosphatase-like B. (PMID: 15024066) Wang B … Shore GC (Molecular and cellular biology 2004) 2 3 4 22 58
  2. 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 58
  3. An Interaction Landscape of Ubiquitin Signaling. (PMID: 28190767) Zhang X … Vermeulen M (Molecular cell 2017) 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. The 3-hydroxyacyl-CoA dehydratases HACD1 and HACD2 exhibit functional redundancy and are active in a wide range of fatty acid elongation pathways. (PMID: 28784662) Sawai M … Kihara A (The Journal of biological chemistry 2017) 3 58

Products for HACD2 Gene

Sources for HACD2 Gene

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