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

    Gene ID: 5264, updated on 27-Nov-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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    See PHYH in Genome Data Viewer
    Location:
    10p13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (13277799..13300064, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (13290862..13313116, complement)
    RS_2024_09 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. Clinical and biochemical heterogeneity in conditions with phytanic acid accumulation. Skjeldal OH, et al. J Neurol Sci, 1987 Jan. PMID 2433405
    2. 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
    3. Phytanoyl-coenzyme A hydroxylase deficiency -- the enzyme defect in Refsum's disease. Jansen GA, et al. N Engl J Med, 1997 Jul 10. PMID 9221344
    4. 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
    5. PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated With Attenuated Refsum Disease. Daich Varela M, et al. Invest Ophthalmol Vis Sci, 2024 Feb 1. PMID 38411969, Free PMC Article

    See all (54) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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