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HACD2 3-hydroxyacyl-CoA dehydratase 2 [ Homo sapiens (human) ]

Gene ID: 201562, updated on 11-Apr-2024

Summary

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Official Symbol
HACD2provided by HGNC
Official Full Name
3-hydroxyacyl-CoA dehydratase 2provided by HGNC
Primary source
HGNC:HGNC:9640
See related
Ensembl:ENSG00000206527 MIM:615939; AllianceGenome:HGNC:9640
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PTPLB
Summary
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]
Expression
Ubiquitous expression in fat (RPKM 34.0), prostate (RPKM 10.4) and 24 other tissues See more
Orthologs
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Genomic context

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See HACD2 in Genome Data Viewer
Location:
3q21.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (123491554..123585053, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (126211843..126305184, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (123210401..123303900, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20392 Neighboring gene MPRA-validated peak4799 silencer Neighboring gene SEC22 homolog A, vesicle trafficking protein Neighboring gene ReSE screen-validated silencer GRCh37_chr3:123014237-123014442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123028841-123029342 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123033477-123034370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123034371-123035262 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123038080-123038986 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123038987-123039893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123047195-123047696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123047697-123048196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123049418-123050205 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123062389-123063058 Neighboring gene adenylate cyclase 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123068286-123068786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123069872-123070850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123104604-123105104 Neighboring gene uncharacterized LOC124909420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123105105-123105605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123130683-123131208 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123132020-123132563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:123166099-123166998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123178428-123178928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123178929-123179429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20393 Neighboring gene MPRA-validated peak4801 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20394 Neighboring gene MYLK antisense RNA 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:123347871-123349070 Neighboring gene Sharpr-MPRA regulatory region 9008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123354794-123355455 Neighboring gene uncharacterized LOC124909421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123368429-123368930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123368931-123369430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:123372559-123373059 Neighboring gene myosin light chain kinase

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 3-hydroxyacyl-CoA dehydratases HACD1 and HACD2 exhibit functional redundancy and are active in a wide range of fatty acid elongation pathways. Sawai M, et al. J Biol Chem, 2017 Sep 15. PMID 28784662, Free PMC Article
  2. 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. Wang B, et al. Mol Cell Biol, 2004 Apr. PMID 15024066, Free PMC Article
  3. 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
  4. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. Shimada M, et al. Hum Genet, 2010 Oct. PMID 20677014
  5. Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs. Almasy KM, et al. Mol Cell Proteomics, 2021. PMID 34186245, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The 3-hydroxyacyl-CoA dehydratase 1/2 form complex with trans-2-enoyl-CoA reductase involved in substrates transfer in very long chain fatty acid elongation.
    Title: The 3-hydroxyacyl-CoA dehydratase 1/2 form complex with trans-2-enoyl-CoA reductase involved in substrates transfer in very long chain fatty acid elongation.
  2. Mutations in HACD1 can result in myopathies in humans; knockout mice lacking Hacd1 develop myopathic phenotypes. Data (including data from studies using knockout mice and cultured cells from knockout mice) suggest that HACD1 and HACD2 exhibit overlapping substrate specificities and thus appear to represent redundant activities in skeletal muscle.
    Title: The 3-hydroxyacyl-CoA dehydratases HACD1 and HACD2 exhibit functional redundancy and are active in a wide range of fatty acid elongation pathways.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Data describe a novel human member of the protein tyrosine phosphatase-like B (PTPLB) family, an integral protein of the endoplasmic reticulum membrane, as a BAP31-interacting protein.
    Title: 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.
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

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3-hydroxyacyl-CoA dehydratase activity EXP
Inferred from Experiment
more info
 PubMed 
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 
NOT enables protein tyrosine phosphatase activity IMP
Inferred from Mutant Phenotype
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 long-chain fatty-acyl-CoA biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in sphingolipid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingolipid biosynthetic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2
Names
protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b
protein-tyrosine phosphatase-like member B
very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase 2
NP_001316712.1
NP_001316713.1
NP_001316715.1
NP_001316716.1
NP_940684.1
XP_047303619.1
XP_047303620.1
XP_047303621.1
XP_054201611.1
XP_054201612.1
XP_054201613.1

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_001329783.2 → NP_001316712.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC020631, AC023165, AC025571

  2. NM_001329784.2 → NP_001316713.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC020631, AC023165, AC025571, AC084039
    Conserved Domains (1) summary
    pfam04387
    Location:5 → 152
    PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

  3. NM_001329786.2 → NP_001316715.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate exons compared to variant 1. The resulting isoform (d) is shorter at the N-teminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
    Source sequence(s)
    AC020631, AC023165, AC025571
    Conserved Domains (1) summary
    pfam04387
    Location:1 → 134
    PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

  4. NM_001329787.2 → NP_001316716.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) is shorter at the N-teminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
    Source sequence(s)
    AC020631, AC023165, AC025571
    Conserved Domains (1) summary
    pfam04387
    Location:1 → 134
    PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

  5. NM_198402.5 → NP_940684.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform b

    See identical proteins and their annotated locations for NP_940684.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AY191814
    Consensus CDS
    CCDS46895.1
    UniProtKB/Swiss-Prot
    Q6Y1H2
    Related
    ENSP00000373153.5, ENST00000383657.10
    Conserved Domains (1) summary
    pfam04387
    Location:85 → 245
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    123491554..123585053 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447663.1 → XP_047303619.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X1

  2. XM_047447665.1 → XP_047303621.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X2

  3. XM_047447664.1 → XP_047303620.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    126211843..126305184 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345636.1 → XP_054201611.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X1

  2. XM_054345638.1 → XP_054201613.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X2

  3. XM_054345637.1 → XP_054201612.1  very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6Y1H2.1 GenPept UniProtKB/Swiss-Prot:Q6Y1H2

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