HACD3 3-hydroxyacyl-CoA dehydratase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HACD3provided by HGNC
Official Full Name: 3-hydroxyacyl-CoA dehydratase 3provided by HGNC
Primary source: HGNC:HGNC:24175
See related: Ensembl:ENSG00000074696 MIM:615940; AllianceGenome:HGNC:24175
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: BIND1; B-IND1; HSPC121; PTPLAD1
Summary: Enables 3-hydroxyacyl-CoA dehydratase activity and enzyme binding activity. Involved in fatty acid biosynthetic process; positive regulation by virus of viral protein levels in host cell; and positive regulation of viral genome replication. Located in endoplasmic reticulum and nuclear membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in brain (RPKM 49.9), adrenal (RPKM 46.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q22.31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (65530463..65578349)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (63339879..63387748)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (65822801..65870687)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PTPLAD1 Regulates PHB-Raf Interaction to Orchestrate Epithelial-Mesenchymal and Mitofusion-Fission Transitions in Colorectal Cancer.
Title: PTPLAD1 Regulates PHB-Raf Interaction to Orchestrate Epithelial-Mesenchymal and Mitofusion-Fission Transitions in Colorectal Cancer.
HACD3 (PTPLAD1) is a new candidate gene for type-2 diabetes risk. HACD3 deletion decreases the autophosphorylation of insulin receptor in vitro. HACD3 may regulate the activity of CDK2 and RAB5C.Overexpression of HACD3 inhibits the tyrosine phosphorylation of CDK2 and RAB5C. HACD3 stimulates the physical association of insulin receptor with RAB11A and may regulate the recycling of insulin receptor to the plasma membrane.
Title: A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes.
Our results indicate that PTPLAD1 (HACD3) is in complex with insulin receptor (IR) in rat's liver and in human HEK293 cells. SiRNA-mediated partial knockdown of PTPLAD1 increased level of IR tyrosine phosphorylation and affect IR endocytosis. PTPLAD1 depletion strongly enhanced insulin effect on Glut2 translocation in HEK293 cells similar to the increase in AKT-ser473 phosphorylation. [PTPLAD1]
Title: The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signaling and the Golgi/endosomes protein network.
Genes in the erythroid differentiation and cell cycle regulation pathways influence interindividual variation in RBC indices. Our results provide insights into the molecular basis underlying variation in RBC traits.
Title: Genetic Loci implicated in erythroid differentiation and cell cycle regulation are associated with red blood cell traits.
These results suggest that an Hsp90-dependent chaperone pathway incorporating hB-ind1 is involved in protein folding in the membranous web for the circumvention of the UPR and that it facilitates HCV replication
Title: Cochaperone activity of human butyrate-induced transcript 1 facilitates hepatitis C virus replication through an Hsp90-dependent pathway.
results suggest that hB-ind1 plays a crucial role in HCV RNA replication and the propagation of JFH1 virus through interaction with viral and host proteins
Title: Human butyrate-induced transcript 1 interacts with hepatitis C virus NS5A and regulates viral replication.
The structure of the B-IND1 gene promoter region was determined.
Title: Human B-ind1 gene promoter: cloning and regulation by histone deacetylase inhibitors.

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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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify protein tyrosine phosphatase-like A domain containing 1 (PTPLAD1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Envelope transmembrane glycoprotein gp41	env	HIV-1 gp41 is identified to have a physical interaction with protein tyrosine phosphatase-like A domain containing 1 (PTPLAD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify protein tyrosine phosphatase-like A domain containing 1 (PTPLAD1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify protein tyrosine phosphatase-like A domain containing 1 (PTPLAD1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify protein tyrosine phosphatase-like A domain containing 1 (PTPLAD1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102970 (e-PCR)
- UniSTS:97304

A004R20 (e-PCR)
- UniSTS:24863

D15S1249 (e-PCR)
- UniSTS:40746

WI-15305 (e-PCR)
- UniSTS:7268

RH46948 (e-PCR)
- UniSTS:49344

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 GTPase activator activity	TAS Traceable Author Statement more info	PubMed
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 JNK cascade	IEA Inferred from Electronic Annotation more info
involved_in Rac protein signal transduction	NAS Non-traceable Author Statement more info	PubMed
involved_in Rho protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in canonical NF-kappaB signal transduction	TAS Traceable Author Statement more info	PubMed
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 negative regulation of intracellular signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by virus of viral protein levels in host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in small GTPase-mediated signal transduction	TAS Traceable Author Statement 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
located_in focal adhesion	HDA more info	PubMed
located_in nuclear membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3

Names: butyrate-induced protein 1; butyrate-induced transcript 1; protein tyrosine phosphatase-like A domain containing 1; protein tyrosine phosphatase-like protein PTPLAD1; protein-tyrosine phosphatase-like A domain-containing protein 1; very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase 3

NP_001398065.1

EC 4.2.1.134

NP_057479.2

EC 4.2.1.134

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)

NM_001411136.1 → NP_001398065.1 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 isoform 2

Status: VALIDATED

Source sequence(s)

AC011846, AC027220

Consensus CDS

CCDS92019.1

UniProtKB/TrEMBL

H3BRL8

Related

ENSP00000456300.1, ENST00000566074.5
NM_016395.4 → NP_057479.2 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 isoform 1

See identical proteins and their annotated locations for NP_057479.2

Status: VALIDATED

Source sequence(s)

AC011846, AC027220

Consensus CDS

CCDS45282.1

UniProtKB/Swiss-Prot

A0PJA1, B4DRF4, Q280Z3, Q6PD63, Q8IUI5, Q8NC86, Q8NCB1, Q96T12, Q9NQA7, Q9P035

UniProtKB/TrEMBL

H3BPZ1

Related

ENSP00000261875.5, ENST00000261875.10

Conserved Domains (2) summary

cd06465
Location:8 → 115

p23_hB-ind1_like; p23_like domain found in human (h) butyrate-induced transcript 1 (B-ind1) and similar proteins. hB-ind1 participates in signaling by the small GTPase Rac1. It binds to Rac1 and enhances different Rac1 effects including activation of nuclear factor (NF) ...

pfam04387
Location:195 → 355

PTPLA; Protein tyrosine phosphatase-like protein, PTPLA