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PHYH phytanoyl-CoA 2-hydroxylase [ Homo sapiens (human) ]

Gene ID: 5264, updated on 5-Nov-2017
Official Symbol
PHYHprovided by HGNC
Official Full Name
phytanoyl-CoA 2-hydroxylaseprovided by HGNC
Primary source
HGNC:HGNC:8940
See related
Ensembl:ENSG00000107537 MIM:602026; Vega:OTTHUMG00000017693
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
RD; LN1; PAHX; LNAP1; PHYH1
Summary
This gene is a member of the PhyH family and encodes a peroxisomal protein that is involved in the alpha-oxidation of 3-methyl branched fatty acids. Specifically, this protein converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene have been associated with Refsum disease (RD) and deficient protein activity has been associated with Zellweger syndrome and rhizomelic chondrodysplasia punctata. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Orthologs
Location:
10p13
Exon count:
10
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (13277796..13300130, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13319796..13342133, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 6, pseudogene Neighboring gene upper zone of growth plate and cartilage matrix associated Neighboring gene chromosome 8 open reading frame 59 pseudogene 1 Neighboring gene selenophosphate synthetase 1

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Alpha-oxidation of phytanate, organism-specific biosystem (from REACTOME)
    Alpha-oxidation of phytanate, organism-specific biosystemPhytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Peroxisomal lipid metabolism, organism-specific biosystem (from REACTOME)
    Peroxisomal lipid metabolism, organism-specific biosystemIn humans, the catabolism of phytanate, pristanate, and very long chain fatty acids as well as the first four steps of the biosynthesis of plasmalogens are catalyzed by peroxisomal enzymes. Defects i...
  • Peroxisome, organism-specific biosystem (from KEGG)
    Peroxisome, organism-specific biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • Peroxisome, conserved biosystem (from KEGG)
    Peroxisome, conserved biosystemPeroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ...
  • fatty acid alpha-oxidation, organism-specific biosystem (from BIOCYC)
    fatty acid alpha-oxidation, organism-specific biosystemGeneral Background The major pathway for fatty acid degradation in organisms ranging from bacteria to humans is fatty acid beta-oxidation. However, pathways for fatty acid alpha-oxidation and &omega...
  • fatty acid alpha-oxidation II, conserved biosystem (from BIOCYC)
    fatty acid alpha-oxidation II, conserved biosystemGeneral Background The major pathway for fatty acid degradation in organisms ranging from bacteria to humans is fatty acid beta-oxidation. However, pathways for fatty acid alpha-oxidation and &omega...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-ascorbic acid binding IEA
Inferred from Electronic Annotation
more info
 
carboxylic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
cofactor binding IDA
Inferred from Direct Assay
more info
PubMed 
ferrous iron binding IDA
Inferred from Direct Assay
more info
PubMed 
phytanoyl-CoA dioxygenase activity IDA
Inferred from Direct Assay
more info
PubMed 
phytanoyl-CoA dioxygenase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
2-oxoglutarate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
fatty acid alpha-oxidation IDA
Inferred from Direct Assay
more info
PubMed 
fatty acid alpha-oxidation TAS
Traceable Author Statement
more info
 
isoprenoid metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
methyl-branched fatty acid metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
peroxisomal matrix TAS
Traceable Author Statement
more info
 
peroxisome IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
phytanoyl-CoA dioxygenase, peroxisomal
Names
phytanic acid oxidase
phytanoil-CoA alpha hydroxylase
phytanoyl-CoA 2 oxoglutarate dioxygenase
phytanoyl-CoA alpha-hydroxylase
NP_001032626.1
NP_001310009.1
NP_001310011.1
NP_001310012.1
NP_001310013.1
NP_006205.1

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

  1. NG_012862.1 RefSeqGene

    Range
    5001..27335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037537.1NP_001032626.1  phytanoyl-CoA dioxygenase, peroxisomal isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream ATG and result in an isoform (b) with a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AL138764, BF509272, BM351828
    Consensus CDS
    CCDS41489.1
    UniProtKB/Swiss-Prot
    O14832
    Related
    ENSP00000380121.2, OTTHUMP00000216226, ENST00000396913.6, OTTHUMT00000046847
    Conserved Domains (1) summary
    pfam05721
    Location:1177
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)
  2. NM_001323080.1NP_001310009.1  phytanoyl-CoA dioxygenase, peroxisomal isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) and variant 2 both encode isoform b.
    Source sequence(s)
    AL138764
    Consensus CDS
    CCDS41489.1
    UniProtKB/Swiss-Prot
    O14832
    Conserved Domains (1) summary
    pfam05721
    Location:1177
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)
  3. NM_001323082.1NP_001310011.1  phytanoyl-CoA dioxygenase, peroxisomal isoform c precursor

    Status: REVIEWED

    Source sequence(s)
    AL138764
    Related
    ENSP00000380126.3, OTTHUMP00000179083, ENST00000396920.7, OTTHUMT00000277005
  4. NM_001323083.1NP_001310012.1  phytanoyl-CoA dioxygenase, peroxisomal isoform d precursor

    Status: REVIEWED

    Source sequence(s)
    AL138764
  5. NM_001323084.1NP_001310013.1  phytanoyl-CoA dioxygenase, peroxisomal isoform e

    Status: REVIEWED

    Source sequence(s)
    AL138764
  6. NM_006214.3NP_006205.1  phytanoyl-CoA dioxygenase, peroxisomal isoform a precursor

    See identical proteins and their annotated locations for NP_006205.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AL138764, BC029512, BF185692, BM351828
    Consensus CDS
    CCDS7097.1
    UniProtKB/Swiss-Prot
    O14832
    Related
    ENSP00000263038.4, OTTHUMP00000019131, ENST00000263038.8, OTTHUMT00000046845
    Conserved Domains (1) summary
    pfam05721
    Location:61277
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

    Range
    13277796..13300130 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018921.2 Alternate CHM1_1.1

    Range
    13319709..13342691 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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