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Aliases for PHYH Gene

Aliases for PHYH Gene

  • Phytanoyl-CoA 2-Hydroxylase 2 3 5
  • Phytanoyl-CoA Alpha-Hydroxylase 3 4
  • Phytanic Acid Oxidase 3 4
  • PAHX 3 4
  • Phytanoyl-CoA Hydroxylase (Refsum Disease) 2
  • Phytanoyl-CoA 2 Oxoglutarate Dioxygenase 3
  • Phytanoyl-CoA Dioxygenase, Peroxisomal 3
  • Phytanoil-CoA Alpha Hydroxylase 3
  • Phytanoyl-CoA Dioxygenase 2
  • Phytanoyl-CoA Hydroxylase 2
  • Refsum Disease 2
  • EC 4
  • LNAP1 3
  • PHYH1 3
  • PhyH 4
  • LN1 3
  • RD 3

External Ids for PHYH Gene

Previous GeneCards Identifiers for PHYH Gene

  • GC10M013302
  • GC10M013470
  • GC10M013323
  • GC10M013359
  • GC10M013319
  • GC10M013232

Summaries for PHYH Gene

Entrez Gene Summary for PHYH Gene

  • 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]

GeneCards Summary for PHYH Gene

PHYH (Phytanoyl-CoA 2-Hydroxylase) is a Protein Coding gene. Diseases associated with PHYH include Refsum Disease, Classic and Retinitis Pigmentosa. Among its related pathways are Metabolism and Peroxisomal lipid metabolism. Gene Ontology (GO) annotations related to this gene include electron transfer activity and cofactor binding.

UniProtKB/Swiss-Prot for PHYH Gene

  • Converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA.

Additional gene information for PHYH Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHYH Gene

Genomics for PHYH Gene

GeneHancer (GH) Regulatory Elements for PHYH Gene

Promoters and enhancers for PHYH Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J013298 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 683.2 +1.4 1399 4.3 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 POLR2B PHYH SEPHS1 ENSG00000239665 GC10P013293
GH10J013345 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25.3 -46.8 -46754 7.3 PKNOX1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF213 SEPHS1 PHYH BTBD7P1 PRPF18 PIR45625 GC10P013355
GH10J013337 Enhancer 0.9 Ensembl ENCODE 26.3 -37.0 -37041 3.9 EBF1 POLR2A SCRT2 PRDM10 RCOR1 ZNF600 IKZF2 RUNX3 CHD2 SCRT1 PHYH SEPHS1 GC10M013327 PIR32930
GH10J013219 Enhancer 0.7 ENCODE 26 +82.3 82291 0.3 HDAC1 CTCF RB1 SAP130 TEAD4 MAX ARID4B SIN3A E4F1 RAD21 PHYH RNU6-6P UCMA GC10P013202
GH10J013270 Enhancer 1.1 Ensembl ENCODE 8.5 +30.6 30607 2.7 FOXA2 ARID4B DMAP1 ZNF48 YY1 ETS1 ZNF143 ZNF548 FOS RXRA ENSG00000273474 PRPF18 PHYH GC10P013279 UCMA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHYH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHYH gene promoter:
  • STAT3
  • Evi-1
  • POU3F2
  • Lhx3a
  • LHX3b

Genomic Locations for PHYH Gene

Genomic Locations for PHYH Gene
24,617 bases
Minus strand
24,617 bases
Minus strand

Genomic View for PHYH Gene

Genes around PHYH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHYH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHYH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHYH Gene

Proteins for PHYH Gene

  • Protein details for PHYH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Phytanoyl-CoA dioxygenase, peroxisomal
    Protein Accession:
    Secondary Accessions:
    • A8MTS8
    • B1ALH5

    Protein attributes for PHYH Gene

    338 amino acids
    Molecular mass:
    38538 Da
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Interacts specifically with the immunophilin FKBP52 and PHYHIP.

    Three dimensional structures from OCA and Proteopedia for PHYH Gene

    Alternative splice isoforms for PHYH Gene


neXtProt entry for PHYH Gene

Post-translational modifications for PHYH Gene

  • Ubiquitination at isoforms=2310 and isoforms=2108
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHYH Gene

Domains & Families for PHYH Gene

Gene Families for PHYH Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PHYH Gene


Suggested Antigen Peptide Sequences for PHYH Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PhyH family.
  • Belongs to the PhyH family.
genes like me logo Genes that share domains with PHYH: view

Function for PHYH Gene

Molecular function for PHYH Gene

UniProtKB/Swiss-Prot Function:
Converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA.
UniProtKB/Swiss-Prot CatalyticActivity:
Phytanoyl-CoA + 2-oxoglutarate + O(2) = 2-hydroxyphytanoyl-CoA + succinate + CO(2).
GENATLAS Biochemistry:
phytanoyl-CoA hydroxylase,41.2kDa,FKBP-associated protein,containing a cleavable peroxisomal targetting signal type 2 (PTS2)

Enzyme Numbers (IUBMB) for PHYH Gene

Phenotypes From GWAS Catalog for PHYH Gene

Gene Ontology (GO) - Molecular Function for PHYH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 9326939
GO:0008198 ferrous iron binding IDA 16186124
GO:0016491 oxidoreductase activity IEA,IBA --
GO:0031406 carboxylic acid binding IDA 16186124
genes like me logo Genes that share ontologies with PHYH: view
genes like me logo Genes that share phenotypes with PHYH: view

Human Phenotype Ontology for PHYH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHYH Gene

MGI Knock Outs for PHYH:
  • Phyh Phyh<tm1Safe>

Animal Model Products

CRISPR Products

miRNA for PHYH Gene

miRTarBase miRNAs that target PHYH

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYH

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for PHYH Gene

Localization for PHYH Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHYH Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHYH gene
Compartment Confidence
peroxisome 5
mitochondrion 3
extracellular 2
cytosol 2
plasma membrane 1
cytoskeleton 1
nucleus 1

Gene Ontology (GO) - Cellular Components for PHYH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005777 peroxisome IDA,IEA 9326939
GO:0005782 peroxisomal matrix TAS --
genes like me logo Genes that share ontologies with PHYH: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PHYH Gene

Pathways & Interactions for PHYH Gene

genes like me logo Genes that share pathways with PHYH: view

Pathways by source for PHYH Gene

1 KEGG pathway for PHYH Gene

UniProtKB/Swiss-Prot O14832-PAHX_HUMAN

  • Pathway: Lipid metabolism; fatty acid metabolism.

Gene Ontology (GO) - Biological Process for PHYH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001561 fatty acid alpha-oxidation TAS --
GO:0006103 2-oxoglutarate metabolic process IDA 16186124
GO:0006629 lipid metabolic process IBA --
GO:0006631 fatty acid metabolic process IEA --
GO:0006720 isoprenoid metabolic process IDA 11555634
genes like me logo Genes that share ontologies with PHYH: view

No data available for SIGNOR curated interactions for PHYH Gene

Drugs & Compounds for PHYH Gene

(10) Drugs for PHYH Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target 581,581
Antihemophilic factor, human recombinant Approved, Investigational Pharma Target, antagonist 0
Lonoctocog alfa Approved, Investigational Pharma Target, antagonist 0
Moroctocog alfa Approved Pharma Target, antagonist 0
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0

(8) Additional Compounds for PHYH Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-2-Hydroxyphytanoyl-CoA
  • (3S)-2-Hydroxyphytanoyl-coenzyme A
  • (3S,7R,11R)-2-Hydroxy-3,7,11,15-tetramethylhexadecanoyl-CoA
  • (3S,7R,11R)-2-Hydroxy-3,7,11,15-tetramethylhexadecanoyl-coenzyme A
  • 2-Hydroxyphytanoyl-coenzyme A
  • FE (II) ion
  • Fe(II)
  • Fe(2+)
  • Ferrous ion
  • Iron ion(2+)
  • 3,7,11,15-Tetramethyl hexadecanoyl CoA
  • 3,7,11,15-Tetramethyl hexadecanoyl coenzyme A
  • Phytanoyl CoA
  • Phytanoyl coenzyme A
  • Phytanoyl-coenzyme A
genes like me logo Genes that share compounds with PHYH: view

Transcripts for PHYH Gene

Unigene Clusters for PHYH Gene

Phytanoyl-CoA 2-hydroxylase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYH

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHYH Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10
SP1: - -
SP2: -
SP3: - -
SP4: -

Relevant External Links for PHYH Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHYH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHYH Gene

mRNA differential expression in normal tissues according to GTEx for PHYH Gene

This gene is overexpressed in Muscle - Skeletal (x7.9) and Liver (x6.2).

Protein differential expression in normal tissues from HIPED for PHYH Gene

This gene is overexpressed in Gallbladder (34.2), Liver (15.1), and Fetal Liver (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PHYH Gene

NURSA nuclear receptor signaling pathways regulating expression of PHYH Gene:


SOURCE GeneReport for Unigene cluster for PHYH Gene:


mRNA Expression by UniProt/SwissProt for PHYH Gene:

Tissue specificity: Expressed in liver, kidney, and T-cells, but not in spleen, brain, heart, lung and skeletal muscle.

Evidence on tissue expression from TISSUES for PHYH Gene

  • Liver(4.6)
  • Nervous system(4.4)
  • Lymph node(2.2)
  • Muscle(2.1)
  • Kidney(2)
  • Skin(2)
  • Stomach(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PHYH Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebrospinal fluid
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • meninges
  • neck
  • nose
  • olfactory bulb
  • clavicle
  • heart
  • heart valve
  • lung
  • spleen
  • arm
  • digit
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • radius
  • shin
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with PHYH: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for PHYH Gene

Orthologs for PHYH Gene

This gene was present in the common ancestor of animals.

Orthologs for PHYH Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PHYH 34 33
  • 99.11 (n)
(Bos Taurus)
Mammalia PHYH 34 33
  • 83.48 (n)
-- 34
  • 77 (a)
(Canis familiaris)
Mammalia LOC478000 33
  • 79.98 (n)
-- 34
  • 77 (a)
-- 34
  • 68 (a)
(Mus musculus)
Mammalia Phyh 16 34 33
  • 79.59 (n)
(Rattus norvegicus)
Mammalia Phyh 33
  • 79.49 (n)
(Monodelphis domestica)
Mammalia PHYH 34
  • 73 (a)
(Ornithorhynchus anatinus)
Mammalia PHYH 34
  • 52 (a)
(Gallus gallus)
Aves PHYH 34 33
  • 65.97 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 66 (a)
-- 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phyh 33
  • 68.42 (n)
Str.15015 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.17548 33
(Danio rerio)
Actinopterygii phyh 34 33
  • 68.17 (n)
PHYH (2 of 2) 34
  • 67 (a)
(Caenorhabditis elegans)
Secernentea CELE_ZK550.6 33
  • 62.12 (n)
ZK550.6 34
  • 56 (a)
ZK550.5 34 35
  • 45 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 58 (a)
Cin.4002 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4002 33
Species where no ortholog for PHYH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PHYH Gene

Gene Tree for PHYH (if available)
Gene Tree for PHYH (if available)
Evolutionary constrained regions (ECRs) for PHYH: view image

Paralogs for PHYH Gene

No data available for Paralogs for PHYH Gene

Variants for PHYH Gene

Sequence variations from dbSNP and Humsavar for PHYH Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs104894173 pathogenic, Refsum disease, adult, 1, Refsum disease (RD) [MIM:266500] 13,288,428(-) C/T coding_sequence_variant, intron_variant, missense_variant
rs104894174 pathogenic, Refsum disease, adult, 1, Refsum disease (RD) [MIM:266500] 13,283,694(-) C/T coding_sequence_variant, missense_variant
rs104894178 pathogenic, likely-pathogenic, Refsum disease, adult, 1, not provided, Retinitis pigmentosa, Refsum disease (RD) [MIM:266500] 13,283,695(-) G/A coding_sequence_variant, missense_variant
rs104894179 pathogenic, Refsum disease, adult, 1, Refsum disease (RD) [MIM:266500] 13,283,713(-) T/G coding_sequence_variant, missense_variant
rs11133 benign, Phytanic acid storage disease 13,278,236(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PHYH Gene

Variant ID Type Subtype PubMed ID
nsv472437 CNV novel sequence insertion 20440878
nsv831788 CNV loss 17160897

Variation tolerance for PHYH Gene

Residual Variation Intolerance Score: 69.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.55; 64.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHYH Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHYH Gene

Disorders for PHYH Gene

MalaCards: The human disease database

(18) MalaCards diseases for PHYH Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
refsum disease, classic
  • rd
retinitis pigmentosa
  • retinitis pigmentosa 1
rhizomelic chondrodysplasia punctata
  • chondrodysplasia punctata, rhizomelic form
hodgkin's lymphoma, mixed cellularity
  • hodgkin lymphoma, mixed cellularity
testicular infarct
  • infarction of testis
- elite association - COSMIC cancer census association via MalaCards
Search PHYH in MalaCards View complete list of genes associated with diseases


  • Refsum disease (RD) [MIM:266500]: A rare autosomal recessive peroxisomal disorder characterized by the accumulation of the branched-chain fatty acid, phytanic acid, in blood and tissues. Cardinal clinical features are retinitis pigmentosa, peripheral neuropathy, cerebellar ataxia, and elevated protein levels in the cerebrospinal fluid (CSF). Half of all patients exhibit generalized, mild to moderate ichthyosis resembling ichthyosis vulgaris. Less constant features are nerve deafness, anosmia, skeletal abnormalities, cataracts and cardiac impairment. {ECO:0000269 PubMed:10709665, ECO:0000269 PubMed:10767344, ECO:0000269 PubMed:14974078, ECO:0000269 PubMed:9326939, ECO:0000269 PubMed:9326940}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PHYH

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PHYH: view

No data available for Genatlas for PHYH Gene

Publications for PHYH Gene

  1. Identification of PAHX, a Refsum disease gene. (PMID: 9326939) Mihalik SJ … Gould SJ (Nature genetics 1997) 2 3 4 22 58
  2. Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease. (PMID: 16186124) McDonough MA … Schofield CJ (The Journal of biological chemistry 2005) 3 4 22 58
  3. Molecular basis of Refsum disease: sequence variations in phytanoyl-CoA hydroxylase (PHYH) and the PTS2 receptor (PEX7). (PMID: 14974078) Jansen GA … Wanders RJ (Human mutation 2004) 3 4 22 58
  4. Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. (PMID: 10767344) Jansen GA … Wanders RJ (Human molecular genetics 2000) 3 4 22 58
  5. Phytanoyl-CoA hydroxylase deficiency. Enzymological and molecular basis of classical Refsum disease. (PMID: 10709665) Jansen GA … Wanders RJ (Advances in experimental medicine and biology 1999) 3 4 22 58

Products for PHYH Gene

Sources for PHYH Gene

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