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

Gene ID: 5264, updated on 5-Mar-2024

Summary

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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; AllianceGenome:HGNC:8940
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
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Genomic context

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Location:
10p13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (13277799..13300064, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (13290862..13313116, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13319799..13342064, 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 H3K4me1 hESC enhancer GRCh37_chr10:13276077-13276987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13341054-13341674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2152 Neighboring gene uncharacterized LOC124902377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3051 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13343766-13344266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3053 Neighboring gene RBIS pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Prognostic role of PHYH for overall survival (OS) in clear cell renal cell carcinoma (ccRCC). Zhengqi Q, et al. Eur J Med Res, 2021 Jan 19. PMID 33468235, Free PMC Article
  2. Cochlear Implantation in Siblings With Refsum's Disease. Stähr K, et al. Ann Otol Rhinol Laryngol, 2017 Aug. PMID 28681609
  3. Non-manifesting Refsum heterozygotes carrying the c.135-2A>G PAHX gene transition. Finsterer J, et al. Neurol Sci, 2008 Jun. PMID 18612766
  4. Studies on the specificity of unprocessed and mature forms of phytanoyl-CoA 2-hydroxylase and mutation of the iron binding ligands. Searls T, et al. J Lipid Res, 2005 Aug. PMID 15930519
  5. Studies on phytanoyl-CoA 2-hydroxylase and synthesis of phytanoyl-coenzyme A. Kershaw NJ, et al. Bioorg Med Chem Lett, 2001 Sep 17. PMID 11549466

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease.
    Title: PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease.
  2. Prognostic role of PHYH for overall survival (OS) in clear cell renal cell carcinoma (ccRCC).
    Title: Prognostic role of PHYH for overall survival (OS) in clear cell renal cell carcinoma (ccRCC).
  3. 3 heterozygous variants: c.85C>T (p.Pro29Ser), c.135-2A>G, and c.768del63bp (p.Phe257Glnfs*16) were found in a family with Refsum's disease.
    Title: Cochlear Implantation in Siblings With Refsum's Disease.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  5. In the absence of elevated phytanic acid concentrations, clinical neurologic abnormalities in heterozygous relatives of Refsum patients are not attributable to heterozygosity for PAHX mutations.
    Title: Non-manifesting Refsum heterozygotes carrying the c.135-2A>G PAHX gene transition.
  6. demonstrate that both unprocessed and processed forms are able to hydroxylate a range of CoA derivatives; site-directed mutagenesis was used to support proposals for the identity of the iron binding istes of PAHX
    Title: Studies on the specificity of unprocessed and mature forms of phytanoyl-CoA 2-hydroxylase and mutation of the iron binding ligands.
  7. substrate specificity of PAHX is broader than expected, so Refsum disease might be characterized by an accumulation of not only phytanic acid but also other 3-alkyl-branched fatty acids
    Title: Further studies on the substrate spectrum of phytanoyl-CoA hydroxylase: implications for Refsum disease?
  8. manner in which phytanoyl-CoA 2-hydroxylase (PAHX) binds to iron(II) and 2-oxoglutarate at its active site distinguishes it from that of the other human 2-oxoglutarate (2OG)-dependent oxygenase
    Title: Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease.
  9. Ten novel PHYH mutations found in Refsum disease patients.
    Title: Molecular basis of Refsum disease: sequence variations in phytanoyl-CoA hydroxylase (PHYH) and the PTS2 receptor (PEX7).
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

Associated conditions

Description Tests
Phytanic acid storage disease
MedGen: C0034960 OMIM: 266500 GeneReviews: Adult Refsum Disease
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

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

General protein information

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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)

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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

  1. NG_012862.1 RefSeqGene

    Range
    5067..27332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037537.2 → NP_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:1 → 177
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  2. NM_001323080.2 → NP_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:1 → 177
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  3. NM_001323082.2 → NP_001310011.1  phytanoyl-CoA dioxygenase, peroxisomal isoform c precursor

    Status: REVIEWED

    Source sequence(s)
    AL138764
    UniProtKB/TrEMBL
    Q6FGQ2
    Related
    ENSP00000380126.3, ENST00000396920.7

  4. NM_001323083.2 → NP_001310012.1  phytanoyl-CoA dioxygenase, peroxisomal isoform d precursor

    Status: REVIEWED

    Source sequence(s)
    AL138764

  5. NM_001323084.2 → NP_001310013.1  phytanoyl-CoA dioxygenase, peroxisomal isoform e

    Status: REVIEWED

    Source sequence(s)
    AL138764

  6. NM_006214.4 → NP_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
    A8MTS8, B1ALH5, O14832
    UniProtKB/TrEMBL
    Q6FGQ2
    Related
    ENSP00000263038.4, ENST00000263038.9
    Conserved Domains (1) summary
    pfam05721
    Location:61 → 277
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    13277799..13300064 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    13290862..13313116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14832.1 GenPept UniProtKB/Swiss-Prot:O14832

Gene LinkOut

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