Human Gene PHYH (ENST00000396920.7)
  Description: phytanoyl-CoA 2-hydroxylase (from HGNC PHYH)
RefSeq Summary (NM_001323082): 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]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000396920.7
Gencode Gene: ENSG00000107537.14
Transcript (Including UTRs)
   Position: hg38 chr10:13,277,843-13,302,412 Size: 24,570 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr10:13,278,301-13,302,007 Size: 23,707 Coding Exon Count: 9 

Page IndexSequence and LinksMalaCardsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:13,277,843-13,302,412)mRNA (may differ from genome)Protein (321 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS

-  MalaCards Disease Associations
  MalaCards Gene Search: PHYH
Diseases sorted by gene-association score: refsum disease* (1633), phyh-related refsum disease* (100), rhizomelic chondrodysplasia punctata (20), hodgkin's lymphoma, mixed cellularity (16), testicular infarct (15), peroxisome disorders (12), rhizomelic chondrodysplasia punctata, type 2 (9), encephalitozoonosis (9), chronic polyneuropathy (7), malignant epithelial mesothelioma (7), ichthyosis vulgaris (7), gastritis, familial giant hypertrophic (7), gastrointestinal lymphoma (5), alpha-methylacyl-coa racemase deficiency (5), aleutian mink disease (4), rhizomelic chondrodysplasia punctata, type 1 (4), peroxisome biogenesis disorder 1b (4), retinitis pigmentosa (3), leber congenital amaurosis (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 75.48 RPKM in Muscle - Skeletal
Total median expression: 814.90 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -141.70405-0.350 Picture PostScript Text
3' UTR -92.90458-0.203 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008775 - Phytyl_CoA_dOase

Pfam Domains:
PF05721 - Phytanoyl-CoA dioxygenase (PhyH)

ModBase Predicted Comparative 3D Structure on B1ALH6
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  KJ897326 - Synthetic construct Homo sapiens clone ccsbBroadEn_06720 PHYH gene, encodes complete protein.
KR709551 - Synthetic construct Homo sapiens clone CCSBHm_00003351 PHYH (PHYH) mRNA, encodes complete protein.
KR709552 - Synthetic construct Homo sapiens clone CCSBHm_00003352 PHYH (PHYH) mRNA, encodes complete protein.
KR709553 - Synthetic construct Homo sapiens clone CCSBHm_00003359 PHYH (PHYH) mRNA, encodes complete protein.
KR709554 - Synthetic construct Homo sapiens clone CCSBHm_00003364 PHYH (PHYH) mRNA, encodes complete protein.
BC029512 - Homo sapiens phytanoyl-CoA 2-hydroxylase, mRNA (cDNA clone MGC:33777 IMAGE:5277185), complete cds.
AF023462 - Homo sapiens peroxisomal phytanoyl-CoA alpha-hydroxylase (PAHX) mRNA, complete cds.
AF112977 - Homo sapiens phytanoil-CoA alpha hydroxylase mRNA, complete cds.
JD433792 - Sequence 414816 from Patent EP1572962.
JD042523 - Sequence 23547 from Patent EP1572962.
DQ891007 - Synthetic construct clone IMAGE:100003637; FLH168466.01X; RZPDo839H0292D phytanoyl-CoA 2-hydroxylase (PHYH) gene, encodes complete protein.
DQ894185 - Synthetic construct Homo sapiens clone IMAGE:100008645; FLH168462.01L; RZPDo839H0291D phytanoyl-CoA 2-hydroxylase (PHYH) gene, encodes complete protein.
CR542055 - Homo sapiens full open reading frame cDNA clone RZPDo834D0836D for gene PHYH, phytanoyl-CoA hydroxylase (Refsum disease); complete cds, without stopcodon.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04146 - Peroxisome

-  Other Names for This Gene
  Alternate Gene Symbols: AF023462, B1ALH6, B1ALH6_HUMAN, ENST00000396920.1, ENST00000396920.2, ENST00000396920.3, ENST00000396920.4, ENST00000396920.5, ENST00000396920.6, RP11-24J20.1-005, uc057rtt.1
UCSC ID: ENST00000396920.7
RefSeq Accession: NM_001323082
Protein: B1ALH6

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PHYH:
refsum (Refsum Disease)
ataxias (Hereditary Ataxia Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.