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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PHYH Gene

protein-coding   GIFtS: 66
GCID: GC10M013319

Phytanoyl-CoA 2-Hydroxylase

(Previous names: phytanoyl-CoA hydroxylase (Refsum disease), phytanoyl-CoA...)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Phytanoyl-CoA 2-Hydroxylase1 2     LN12
PAHX2 3 5     LNAP12
Phytanic Acid Oxidase2 3     PHYH12
Phytanoyl-CoA Alpha-Hydroxylase2 3     RD2
EC 1.14.11.183 8     Phytanoil-CoA Alpha Hydroxylase2
Phytanoyl-CoA Dioxygenase1     Phytanoyl-CoA 2 Oxoglutarate Dioxygenase2
Phytanoyl-CoA Hydroxylase1     Phytanoyl-CoA Dioxygenase, Peroxisomal2
Phytanoyl-CoA Hydroxylase (Refsum Disease)1     PhyH3
Refsum Disease1     

External Ids:    HGNC: 89401   Entrez Gene: 52642   Ensembl: ENSG000001075377   OMIM: 6020265   UniProtKB: O148323   

Export aliases for PHYH gene to outside databases

Previous GC identifers: GC10M013302 GC10M013470 GC10M013323 GC10M013359 GC10M013232


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and phyh-related refsum disease, and among its related super-pathways are fatty acid alpha-oxidation II and Metabolic pathways. GO annotations related to this gene include electron carrier activity and L-ascorbic acid binding.

UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832
Function: Converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NT_008705.16  NC_018921.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PHYH gene promoter:
         LHX3b/Lhx3b   LHX3a/Lhx3a   STAT3   POU3F2   Evi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPHYH promoter sequence
   Search SABiosciences Chromatin IP Primers for PHYH

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PHYH


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 10p13   Ensembl cytogenetic band:  10p13   HGNC cytogenetic band: 10p13

PHYH Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHYH gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M013319:  view genomic region     (about GC identifiers)

Start:
13,319,796 bp from pter      End:
13,344,412 bp from pter
Size:
24,617 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832 (See protein sequence)
Recommended Name: Phytanoyl-CoA dioxygenase, peroxisomal precursor  
Size: 338 amino acids; 38538 Da
Cofactor: Iron
Cofactor: Ascorbate
Subunit: Interacts specifically with the immunophilin FKBP52 and PHYHIP
Subcellular location: Peroxisome
1 PDB 3D structure from and Proteopedia for PHYH:
2A1X (3D)    
Secondary accessions: A8MTS8 B1ALH5
Alternative splicing: 2 isoforms:  O14832-1   O14832-2   (No experimental confirmation available. Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for PHYH: NX_O14832

Explore proteomics data for PHYH at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O14832

  • 4 DME Specific Peptides for PHYH (O14832)
     MLINKPPD  GFRKAISCH  YPKWEGGVNK  RNNGCLVVLPGTHKG 

    PHYH Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PHYH Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001032626.1  NP_006205.1  

    ENSEMBL proteins: 
     ENSP00000380121   ENSP00000263038   ENSP00000380126   ENSP00000412525   ENSP00000420117  
    Reactome Protein details: O14832
    Human Recombinant Protein Products for PHYH: 
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    Novus Biologicals PHYH Protein
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    Sino Biological Recombinant Protein for PHYH
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PHYH 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--
    GO:0005777peroxisome IDA9326939
    GO:0005782peroxisomal matrix TAS--

    PHYH for ontologies           About GeneDecksing



    PHYH Antibody Products: 
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    LSBio Antibodies in human, mouse, rat for PHYH 

    Assay Products for PHYH: 
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    Cloud-Clone Corp. ELISAs for PHYH 
    Cloud-Clone Corp. CLIAs for PHYH


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR008775 Phytyl_CoA_dOase

    Graphical View of Domain Structure for InterPro Entry O14832

    ProtoNet protein and cluster: O14832

    1 Blocks protein domain: IPB008775 Phytanoyl-CoA dioxygenase

    UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832
    Similarity: Belongs to the PhyH family


    PHYH for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PAHX_HUMAN, O14832
    Function: Converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA
    Catalytic activity: Phytanoyl-CoA + 2-oxoglutarate + O(2) = 2-hydroxyphytanoyl-CoA + succinate + CO(2)

         Genatlas biochemistry entry for PHYH:
    phytanoyl-CoA hydroxylase,41.2kDa,FKBP-associated protein,containing a cleavable peroxisomal targetting signal
    type 2 (PTS2)

         Enzyme Number (IUBMB): EC 1.14.11.181 2

         Gene Ontology (GO): 5/8 molecular function terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0005515protein binding IPI10051602
    GO:0009055electron carrier activity TAS8954107
    GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen ----
    GO:0031418L-ascorbic acid binding IEA--
         
    PHYH for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 1 allele(MGI details for Phyh):
     adipose tissue  behavior/neurological  growth/size  homeostasis/metabolism  immune system 
     liver/biliary system  nervous system  reproductive system 

    PHYH for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Phyhtm1Safe for PHYH

       inGenious Targeting Laboratory - Custom generated mouse model solutions for PHYH 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for PHYH

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PHYH 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PHYH 

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate PHYH:
    hsa-miR-1276
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHYH


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for PHYH About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Alpha-oxidation of phytanate
    fatty acid alpha-oxidation II0.50
    Alpha-oxidation of phytanate0.50
    2Metabolism
    Metabolism0.40
    Metabolism of lipids and lipoproteins0.34
    3Peroxisomal lipid metabolism
    Peroxisomal lipid metabolism0.38
    4Peroxisome
    Peroxisome

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for PHYH
        fatty acid alpha-oxidation II


    4        Reactome Pathways for PHYH
        Alpha-oxidation of phytanate
    Metabolism
    Peroxisomal lipid metabolism
    Metabolism of lipids and lipoproteins


    1         Kegg Pathway  (Kegg details for PHYH):
        Peroxisome

    UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832
    Pathway: Lipid metabolism; fatty acid metabolism


    PHYH for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for PHYH

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    5/18 Interacting proteins for PHYH (O148321, 2, 3 ENSP000002630384) via UniProtKB, MINT, STRING, and/or I2D (see all 18)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    COPS3Q9UNS21, 3, ENSP000002687174EBI-721853,EBI-350590 I2D: score=2 STRING: ENSP00000268717
    WRAP73Q9P2S51, 3, ENSP000002707084EBI-721853,EBI-1054904 I2D: score=2 STRING: ENSP00000270708
    TOM1L1O756742, 3MINT-63080 I2D: score=5 
    WDR8Q9P2S51, 3EBI-721853,EBI-1054904 I2D: score=2 
    MAGEA11P433642, 3, ENSP000003473584MINT-66763 I2D: score=5 STRING: ENSP00000347358
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001561fatty acid alpha-oxidation TAS--
    GO:0006720isoprenoid metabolic process IDA11555634
    GO:0044255cellular lipid metabolic process TAS--
    GO:0044281small molecule metabolic process TAS--
    GO:0097089methyl-branched fatty acid metabolic process IDA10744784

    PHYH for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    PHYH for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PHYH (PAHX)

    8 HMDB Compounds for PHYH    About this table
    CompoundSynonyms CAS #PubMed Ids
    2-Hydroxyphytanoyl-CoA2-Hydroxyphytanoyl-CoA (see all 10)172787-73-4--
    Ascorbic acid(+)-ascorbate (see all 140)50-81-7--
    Carbon dioxideCarbon oxide (see all 5)124-38-9--
    IronArmco iron (see all 19)7439-89-6--
    Oxoglutaric acid2-Ketoglutarate (see all 9)328-50-7--
    OxygenOxygen (see all 5)7782-44-7--
    Phytanoyl-CoAPhytanoyl-coenzyme A (see all 8)146622-45-9--
    Succinic acid1,2-Ethanedicarboxylate (see all 11)110-15-6--

    2 DrugBank Compounds for PHYH    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Antihemophilic FactorAHF (see all 3)--targetantagonist17139284 11574539 17016423
    Vitamin CAscorbate (see all 6)50-81-7target--17139284 17016423

    8 Novoseek inferred chemical compound relationships for PHYH gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    2-hydroxyphytanoyl-coa 97 5 10588950 (1), 8954107 (1), 11341778 (1), 11948235 (1)
    phytanic acid 96.7 22 10866807 (5), 10588950 (2), 8954107 (2), 18612766 (2) (see all 12)
    alpha-ketoglutarate 54 11 16186124 (5), 9326939 (1), 17956235 (1)
    fatty acid 33.3 2 17956237 (1)
    paraffin 26.4 1 2331047 (1)
    histidine 11.1 1 16186124 (1)
    iron 1.06 4 9326939 (1), 15930519 (1), 16186124 (1)
    lipid 0 1 15452860 (1)

    Search CenterWatch for drugs/clinical trials and news about PHYH / PAHX

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PHYH gene (2 alternative transcripts): 
    NM_001037537.1  NM_006214.3  

    Unigene Cluster for PHYH:

    Phytanoyl-CoA 2-hydroxylase
    Hs.498732  [show with all ESTs]
    Unigene Representative Sequence: NM_001037537
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000396913(uc001ime.3) ENST00000263038(uc001imf.3) ENST00000396920
    ENST00000453759 ENST00000479604 ENST00000464049 ENST00000463730

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate PHYH:
    hsa-miR-1276
    SwitchGear 3'UTR luciferase reporter plasmidPHYH 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AF023462.1 AF112977.1 BC021011.1 BC029512.1 CR542055.1 

    12 DOTS entries:

    DT.216103  DT.75120414  DT.100796169  DT.100796173  DT.92432991  DT.95107144  DT.100796168  DT.100796171 
    DT.121216358  DT.86848595  DT.92432993  DT.95268160 

    24/201 AceView cDNA sequences (see all 201):

    CR591194 CR610525 BU730211 T32499 N72414 AV653048 CR623416 CR600223 
    T81584 CR597553 BM985421 CK822288 CB164091 BM701313 CR623967 BC021011 
    Z43616 H99693 BG771955 F18906 BM674280 AW316699 BF185692 AA772166 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PHYH    About this scheme

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


    ECgene alternative splicing isoforms for PHYH

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PHYH expression in normal human tissues (normalized intensities)      PHYH embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGTCCAAAT
    PHYH Expression
    About this image


    PHYH expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/31 selected tissues (see all 31) fully expand
     
     Brain (Nervous System)    fully expand to see all 9 entries
             Cerebral Cortex
             brain/midbrain   
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Nose (Sensory Organs)    fully expand to see all 3 entries
             nasopharynx ; respiratory epithelial cells   
             sensory organ/nose/nasal cavity   
     
     Kidney (Urinary System)    fully expand to see all 3 entries
             Metanephros
             kidney ; cells in tubules   

    See PHYH Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PHYH

    SOURCE GeneReport for Unigene cluster: Hs.498732

    UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832
    Tissue specificity: Expressed in liver, kidney, and T-cells, but not in spleen, brain, heart, lung and skeletal
    muscle

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHYH

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for PHYH gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phyh1 , 5 phytanoyl-CoA hydroxylase1, 5 79.59(n)1
    78.11(a)1
      2 (3.06 cM)5
    169221  NM_010726.21  NP_034856.11 
     49190195 
    chicken
    (Gallus gallus)
    Aves PHYH1 phytanoyl-CoA 2-hydroxylase 65.97(n)
    64.48(a)
      426601  XM_424238.3  XP_424238.3 
    lizard
    (Anolis carolinensis)
    Reptilia PHYH6
    --
    --
    67(a)
    66(a)
    many → 1
    many → 1
    5(89977349-89997444)
    5(90012036-90029690)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.175482 Xenopus laevis transcribed sequence with weak similarity more 75.94(n)    BU899751.1 
    zebrafish
    (Danio rerio)
    Actinopterygii phyh1 phytanoyl-CoA 2-hydroxylase 68.17(n)
    69.07(a)
      550521  NM_001017823.1  NP_001017823.1 
    worm
    (Caenorhabditis elegans)
    Secernentea ZK550.53
    CELE_ZK550.61
    Protein ZK550.61 51(a)3
    62.12(n)1
    61.43(a)1
      IV(17257748-17259527)3
    1785031  NM_070661.21  NP_503062.11 


    ENSEMBL Gene Tree for PHYH (if available)
    TreeFam Gene Tree for PHYH (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/686 SNPs in PHYH are shown (see all 686)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0174854
    Refsum disease (RD)4--see VAR_0174852 D G mis40--------
    VAR_0174904
    Refsum disease (RD)4--see VAR_0174902 H Y mis40--------
    VAR_0055264
    Refsum disease (RD)4--see VAR_0055262 R W mis40--------
    VAR_0174874
    Refsum disease (RD)4--see VAR_0174872 E Q mis40--------
    VAR_0186194
    Refsum disease (RD)4--see VAR_0186192 N Y mis40--------
    VAR_0174834
    Refsum disease (RD)4--see VAR_0174832 P S mis40--------
    VAR_0186314
    Refsum disease (RD)4--see VAR_0186312 H R mis40--------
    VAR_0174894
    Refsum disease (RD)4--see VAR_0174892 G S mis40--------
    VAR_0055254
    Refsum disease (RD)4--see VAR_0055252 N H mis40--------
    VAR_0174884
    Refsum disease (RD)4--see VAR_0174882 I F mis40--------

    HapMap Linkage Disequilibrium report for PHYH (13319796 - 13344412 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for PHYH:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv831788CNV Loss17160897
    nsv894886CNV Loss21882294


    Human Gene Mutation Database (HGMD): PHYH
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PHYH
    DNA2.0 Custom Variant and Variant Library Synthesis for PHYH

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 602026   
    OMIM disorders: 266500  
    UniProtKB/Swiss-Prot: PAHX_HUMAN, O14832
  • 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. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 20/26 diseases for PHYH (see all 26):    About MalaCards
    refsum disease    phyh-related refsum disease    aleutian mink disease    testicular infarct
    rhizomelic chondrodysplasia punctata type 2    peroxisome disorders    rhizomelic chondrodysplasia punctata    peroxisomal disease
    chondrodysplasia    infantile refsum disease    zellweger syndrome    cerebellar ataxia
    adrenoleukodystrophy    lupus nephritis    peripheral neuropathy    ichthyosis
    nephritis    retinitis pigmentosa    alzheimer's disease    retinitis

    6 diseases from the University of Copenhagen DISEASES database for PHYH:
    Refsum disease     Lymphoma     Rhizomelic chondrodysplasia punctata     Zellweger syndrome
    Infantile refsum disease     Retinitis pigmentosa

    PHYH for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    7 Novoseek inferred disease relationships for PHYH gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    refsum disease 97.1 33 9326939 (3), 17956235 (2), 10951529 (2), 14974078 (2) (see all 19)
    chondrodysplasia punctata rhizomelic 83.2 1 9266377 (1)
    peroxisomal disorders 83 1 8341225 (1)
    retinitis pigmentosa 65 1 17905308 (1)
    lymphoma follicular 45.7 2 2179300 (1), 1689087 (1)
    lymphoma 3.86 1 2179300 (1)
    alzheimers disease 1.56 2 2251906 (1), 1685745 (1)

    GeneTests: PHYH
    GeneReviews: PHYH
    Genetic Association Database (GAD): PHYH
    Human Genome Epidemiology (HuGE) Navigator: PHYH (3 documents)

    Export disorders for PHYH gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PHYH gene, integrated from 9 sources (see all 77):
    (articles sorted by number of sources associating them with PHYH)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of PAHX, a Refsum disease gene. (PubMed id 9326939)1, 2, 3, 9 Mihalik S.J....Gould S.J. (1997)
    2. Roles of phytanoyl-CoA alpha-hydroxylase in mediating the expression of human coagulation factor VIII. (PubMed id 11574539)1, 7, 9 Chen C....Gu J. (2001)
    3. Molecular basis of Refsum disease: sequence variations in phytanoyl- CoA hydroxylase (PHYH) and the PTS2 receptor (PEX7). (PubMed id 14974078)1, 2, 9 Jansen G.A.... Wanders R.J.A. (2004)
    4. Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease. (PubMed id 16186124)1, 2, 9 McDonough M.A....Schofield C.J. (2005)
    5. Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. (PubMed id 10767344)1, 2, 9 Jansen G.A.... Wanders R.J.A. (2000)
    6. Refsum disease is caused by mutations in the phytanoyl-CoA hydroxylase gene. (PubMed id 9326940)1, 2, 9 Jansen G.A....Wanders R.J.A. (1997)
    7. Phytanoyl-CoA hydroxylase deficiency. Enzymological and molecular basis of classical Refsum disease. (PubMed id 10709665)1, 2, 9 Jansen G.A.... Wanders R.J.A. (1999)
    8. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (2010)
    9. Sequential use of transcriptional profiling, expressi on quantitative trait mapping, and gene association implicates MMP20 in human k idney aging. (PubMed id 19834535)1, 4 Wheeler H.E....Kim S.K. (2009)
    10. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 5264 HGNC: 8940 AceView: PHYH Ensembl:ENSG00000107537 euGenes: HUgn5264
    ECgene: PHYH Kegg: 5264 H-InvDB: PHYH

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PHYH Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PHYH

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PHYH gene:
    Search GeneIP for patents involving PHYH

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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