HACD1 3-hydroxyacyl-CoA dehydratase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HACD1provided by HGNC
Official Full Name: 3-hydroxyacyl-CoA dehydratase 1provided by HGNC
Primary source: HGNC:HGNC:9639
See related: Ensembl:ENSG00000165996 MIM:610467; AllianceGenome:HGNC:9639
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: CAP; MYONP; PTPLA; CMYO11; CMYP11
Summary: The protein encoded by this gene contains a characteristic catalytic motif of the protein tyrosine phosphatases (PTPs) family. The PTP motif of this protein has the highly conserved arginine residue replaced by a proline residue; thus it may represent a distinct class of PTPs. Members of the PTP family are known to be signaling molecules that regulate a variety of cellular processes. This gene was preferentially expressed in both adult and fetal heart. A much lower expression level was detected in skeletal and smooth muscle tissues, and no expression was observed in other tissues. The tissue specific expression in the developing and adult heart suggests a role in regulating cardiac development and differentiation. [provided by RefSeq, Jul 2008]
Expression: Broad expression in heart (RPKM 20.1), prostate (RPKM 5.4) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10p12.33

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (17589032..17617374, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (17607536..17635876, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (17631031..17659373, complement)

Chromosome 10 - NC_000010.11 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?

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.
Biallelic loss-of-function HACD1 variants are a bona fide cause of congenital myopathy.
Title: Biallelic loss-of-function HACD1 variants are a bona fide cause of congenital myopathy.
Longitudinal analyses in myopathic Labrador retrievers reveal several membrane-associated defects, including ultrastructural triads dysmorphogenesis and mitochondrial mislocalization in Labrador retrievers with deficiencies in the canine HACD1 gene.
Title: Progressive Structural Defects in Canine Centronuclear Myopathy Indicate a Role for HACD1 in Maintaining Skeletal Muscle Membrane Systems.
Labrador retrievers carrying two copies of a unique canine HACD1 loss-of-function allele that recently disseminated worldwide, are all affected by a congenital myopathy, confirming its role in muscle development.
Title: Centronuclear myopathy in Labrador retrievers: a recent founder mutation in the PTPLA gene has rapidly disseminated worldwide.
A loss-of-function mutation in the canine ortholog of HACD1 that was identified by genetic mapping in a French pedigree of Labrador retrievers causes a congenital myopathy named centronuclear myopathy (CNM) in Labrador retrievers.
Title: SINE exonic insertion in the PTPLA gene leads to multiple splicing defects and segregates with the autosomal recessive centronuclear myopathy in dogs.
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.
These data indicate that HACD1 is necessary for muscle function.
Title: Congenital myopathy is caused by mutation of HACD1.
PTPLA-CAP expression was limited to cementum cells; promoted gingival fibroblast attachment. PTPLA-CAP is splice variant of PTPLA, and that, in the periodontium, cementum and cementum cells express this variant.
Title: Isolation of protein-tyrosine phosphatase-like member-a variant from cementum.
HACD1 is 3-hydroxyacyl-CoA dehydratase involved in elongation of very long-chain fatty acids. HACD1 (K64Q) exhibits normal enzyme activity, intracellular localization and interaction with other VLCFA enzymes, with no negative effect on VLCFA elongation
Title: Characterization of HACD1 K64Q mutant found in arrhythmogenic right ventricular dysplasia patients.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital myopathy 11 MedGen: C3151531 OMIM: 619967 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-56539 (e-PCR)
- UniSTS:4186

D1S1423 (e-PCR)
- UniSTS:149619

STS-N24848 (e-PCR)
- UniSTS:64479

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 hydroxyapatite 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
enables very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cementum mineralization	IDA Inferred from Direct Assay 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 long-chain fatty-acyl-CoA biosynthetic process	TAS Traceable Author Statement more info
involved_in positive regulation of cell-substrate adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed
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
located_in 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 1

Names: cementum attachment protein; protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A; very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase 1

NP_055056.3

EC 4.2.1.134

XP_005252698.1

EC 4.2.1.134

XP_054223116.1

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.

Genomic

NG_041789.1 RefSeqGene

Range

5001..33343

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_014241.4 → NP_055056.3 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 1

See identical proteins and their annotated locations for NP_055056.3

Status: REVIEWED

Source sequence(s)

AC069542, AW022173, AY455942, BC010353

Consensus CDS

CCDS7121.1

UniProtKB/Swiss-Prot

B0YJ80, B0YJ81, Q6JIC5, Q96FW7, Q9HB93, Q9UHX2

Related

ENSP00000355308.3, ENST00000361271.8

Conserved Domains (1) summary

pfam04387
Location:119 → 278

PTPLA; Protein tyrosine phosphatase-like protein, PTPLA

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

17589032..17617374 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005252641.5 → XP_005252698.1 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 1 isoform X1

Conserved Domains (1) summary

pfam04387
Location:125 → 242

PTPLA; Protein tyrosine phosphatase-like protein, PTPLA