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

Gene ID: 5264, updated on 1-Aug-2020

Summary

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
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]
Expression
Broad expression in liver (RPKM 137.6), kidney (RPKM 65.7) and 17 other tissues See more
Orthologs

Genomic context

See PHYH in Genome Data Viewer
Location:
10p13
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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 RBIS pseudogene 1 Neighboring gene selenophosphate synthetase 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-ascorbic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
carboxylic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
ferrous iron binding IDA
Inferred from Direct Assay
more info
PubMed 
phytanoyl-CoA dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phytanoyl-CoA dioxygenase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
2-oxobutyrate catabolic process IEA
Inferred from Electronic Annotation
more info
 
2-oxoglutarate metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
fatty acid alpha-oxidation IBA
Inferred from Biological aspect of Ancestor
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 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
9+0 non-motile cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
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 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5067..27332
    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, ENST00000396913.6
    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, ENST00000396920.7
  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_006214.4NP_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, BM351828
    Consensus CDS
    CCDS7097.1
    UniProtKB/Swiss-Prot
    O14832
    Related
    ENSP00000263038.4, ENST00000263038.9
    Conserved Domains (1) summary
    pfam05721
    Location:61277
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

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