HACL1 2-hydroxyacyl-CoA lyase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HACL1provided by HGNC
Official Full Name: 2-hydroxyacyl-CoA lyase 1provided by HGNC
Primary source: HGNC:HGNC:17856
See related: Ensembl:ENSG00000131373 MIM:604300; AllianceGenome:HGNC:17856
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: HPCL; HPCL2; PHYH2; 2-HPCL
Summary: Enables several functions, including 2-hydroxyacyl-CoA lyase activity; ATP binding activity; and cation binding activity. Involved in fatty acid alpha-oxidation; phytanic acid metabolic process; and protein targeting to peroxisome. Located in nucleoplasm and peroxisome. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Ubiquitous expression in duodenum (RPKM 25.3), testis (RPKM 14.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (15560699..15601569, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (15563097..15603888, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (15602206..15643076, complement)

Chromosome 3 - NC_000003.12 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 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?

Data show that a easy assay for 2-hydroxyacyl-CoA lyase (HACL1) and sphingosine-1-phosphate lyase (SGPL1) activities was developed.
Title: RP-HPLC-fluorescence analysis of aliphatic aldehydes: application to aldehyde-generating enzymes HACL1 and SGPL1.
Transport of thiamine pyrophosphate into peroxisomes is dependent on HACL1 import, without requirement of a specific solute transporter.
Title: Role of thiamine pyrophosphate in oligomerisation, functioning and import of peroxisomal 2-hydroxyacyl-CoA lyase.
2-hydroxyphytanoyl-CoA lyase has a role in the breakdown of long chain 2-hydroxyfatty acids
Title: Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the alpha-oxidation of straight chain fatty acids.
peroxisomal thiamine-pyrophosphate depending enzyme required for the degradation of phytanic acid, catalyzing the cleavage of 2-hydroxyphytanoyl-CoA lyase into formyl-CoA and pristanal
Title: Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids.

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 2-hydroxyacyl-CoA lyase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables 2-hydroxyphytanoyl-CoA lyase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables carbon-carbon lyase activity	IDA Inferred from Direct Assay more info	PubMed
enables carbon-carbon lyase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables thiamine pyrophosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables thiamine pyrophosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables thiamine pyrophosphate binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in fatty acid alpha-oxidation	IBA Inferred from Biological aspect of Ancestor more info
involved_in fatty acid alpha-oxidation	IDA Inferred from Direct Assay more info	PubMed
involved_in fatty acid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in methyl-branched fatty acid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in phytanic acid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein targeting to peroxisome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in peroxisomal matrix	TAS Traceable Author Statement more info
is_active_in peroxisome	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 2-hydroxyacyl-CoA lyase 1

Names: 1600020H07Rik; 2-hydroxyphytanol-CoA lyase; 2-hydroxyphytanoyl-CoA lyase; phytanoyl-CoA 2-hydroxylase 2; phytanoyl-CoA hydroxylase 2

NP_001271342.1

EC 4.1.2.63

NP_001271344.1

EC 4.1.2.63

NP_001271345.1

EC 4.1.2.63

NP_036392.2

EC 4.1.2.63

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_001284413.2 → NP_001271342.1 2-hydroxyacyl-CoA lyase 1 isoform b

See identical proteins and their annotated locations for NP_001271342.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.

Source sequence(s)

AA643224, AC027129, AK301546, DA609383

Consensus CDS

CCDS68360.1

UniProtKB/TrEMBL

B4DXR1

Related

ENSP00000390699.2, ENST00000456194.6

Conserved Domains (1) summary

PRK09259
Location:7 → 536

PRK09259; putative oxalyl-CoA decarboxylase; Validated
NM_001284415.2 → NP_001271344.1 2-hydroxyacyl-CoA lyase 1 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two alternate in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.

Source sequence(s)

AA643224, AC027129, AJ131753, AK302086, BC001627, DA609383

Consensus CDS

CCDS68362.1

UniProtKB/TrEMBL

B4DXR1

Related

ENSP00000404883.2, ENST00000457447.6

Conserved Domains (4) summary

cd07035
Location:19 → 146

TPP_PYR_POX_like; Pyrimidine (PYR) binding domain of POX and related proteins

PRK09259
Location:7 → 503

PRK09259; putative oxalyl-CoA decarboxylase; Validated

cd02004
Location:317 → 500

TPP_BZL_OCoD_HPCL; Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL ...

pfam00205
Location:180 → 305

TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain
NM_001284416.2 → NP_001271345.1 2-hydroxyacyl-CoA lyase 1 isoform d

See identical proteins and their annotated locations for NP_001271345.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks three alternate exons that result in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.

Source sequence(s)

AA643224, AC027129, AK301990, DA609383

Consensus CDS

CCDS68361.1

UniProtKB/TrEMBL

B4DXR1

Related

ENSP00000403656.2, ENST00000451445.6

Conserved Domains (4) summary

cd07035
Location:19 → 103

TPP_PYR_POX_like; Pyrimidine (PYR) binding domain of POX and related proteins

PRK09259
Location:7 → 481

PRK09259; putative oxalyl-CoA decarboxylase; Validated

cd02004
Location:295 → 478

TPP_BZL_OCoD_HPCL; Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL ...

pfam00205
Location:124 → 250

TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain
NM_012260.4 → NP_036392.2 2-hydroxyacyl-CoA lyase 1 isoform a

See identical proteins and their annotated locations for NP_036392.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AA643224, AC027129, AJ131753, BC001627, DA609383

Consensus CDS

CCDS2627.1

UniProtKB/Swiss-Prot

B4DWI1, B4DXI5, E9PEN4, Q9BV42, Q9P0A2, Q9UJ83

UniProtKB/TrEMBL

B4DXR1

Related

ENSP00000323811.5, ENST00000321169.10

Conserved Domains (1) summary

cl28198
Location:7 → 563

IlvB; Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]

RNA

NR_104315.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks two alternate exons in the central region, compared to variant 1. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA643224, AC027129, BC001627, BC007440, DA609383

Related

ENST00000383779.8