Aliases for PHYHD1 Gene

Aliases for PHYHD1 Gene

  • Phytanoyl-CoA Dioxygenase Domain Containing 1 2 3 5
  • Phytanoyl-CoA Dioxygenase Domain-Containing Protein 1 3 4
  • EC 1.-.-.- 4
  • MGC16638 2
  • PHYHD1 5

External Ids for PHYHD1 Gene

Previous GeneCards Identifiers for PHYHD1 Gene

  • GC09P127059
  • GC09P128762
  • GC09P130722
  • GC09P131683
  • GC09P101290

Summaries for PHYHD1 Gene

GeneCards Summary for PHYHD1 Gene

PHYHD1 (Phytanoyl-CoA Dioxygenase Domain Containing 1) is a Protein Coding gene. Diseases associated with PHYHD1 include Ehlers-Danlos Syndrome, Hypermobility Type. Gene Ontology (GO) annotations related to this gene include dioxygenase activity.

UniProtKB/Swiss-Prot Summary for PHYHD1 Gene

  • Isoform 1 has alpha-ketoglutarate-dependent dioxygenase activity. Does not show detectable activity towards fatty acid CoA thioesters. Is not expected to be active with phytanoyl CoA. Isoform 2 and isoform 3 probably lack enzyme activity.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHYHD1 Gene

Genomics for PHYHD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PHYHD1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHYHD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHYHD1

Top Transcription factor binding sites by QIAGEN in the PHYHD1 gene promoter:
  • c-Myc
  • Max1
  • Pax-2
  • Pax-2a
  • ZID

Genomic Locations for PHYHD1 Gene

Latest Assembly
21,076 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
21,060 bases
Plus strand

(GRCh37/hg19 by Ensembl)
21,147 bases
Plus strand

Genomic View for PHYHD1 Gene

Genes around PHYHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHYHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHYHD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHYHD1 Gene

Proteins for PHYHD1 Gene

  • Protein details for PHYHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Phytanoyl-CoA dioxygenase domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • A6PWN9
    • A6PWP0
    • B3KT57
    • B4E3X8
    • Q5SRE9
    • Q5SRF0
    • Q7Z623
    • Q7Z7P9
    • Q96GM4

    Protein attributes for PHYHD1 Gene

    291 amino acids
    Molecular mass:
    32411 Da
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PHYHD1 Gene

    Alternative splice isoforms for PHYHD1 Gene


neXtProt entry for PHYHD1 Gene

Post-translational modifications for PHYHD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

  • Abcam antibodies for PHYHD1

No data available for DME Specific Peptides for PHYHD1 Gene

Domains & Families for PHYHD1 Gene

Gene Families for PHYHD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHYHD1 Gene

  • Phytanoyl-CoA dioxygenase

Suggested Antigen Peptide Sequences for PHYHD1 Gene

GenScript: Design optimal peptide antigens:
  • Phytanoyl-CoA dioxygenase domain containing 1 (B7ZCD9_HUMAN)
  • Phytanoyl-CoA dioxygenase domain-containing protein 1 (PHYD1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PhyH family. PHYHD1 subfamily.
  • Belongs to the PhyH family. PHYHD1 subfamily.
genes like me logo Genes that share domains with PHYHD1: view

Function for PHYHD1 Gene

Molecular function for PHYHD1 Gene

UniProtKB/Swiss-Prot Function:
Isoform 1 has alpha-ketoglutarate-dependent dioxygenase activity. Does not show detectable activity towards fatty acid CoA thioesters. Is not expected to be active with phytanoyl CoA. Isoform 2 and isoform 3 probably lack enzyme activity.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activity is increased by ascorbate. Inhibited by myristoyl-CoA.

Enzyme Numbers (IUBMB) for PHYHD1 Gene

Phenotypes From GWAS Catalog for PHYHD1 Gene

Gene Ontology (GO) - Molecular Function for PHYHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21044950
GO:0016491 oxidoreductase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
genes like me logo Genes that share ontologies with PHYHD1: view
genes like me logo Genes that share phenotypes with PHYHD1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYHD1

Clone products for research

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PHYHD1 Gene

Localization for PHYHD1 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 PHYHD1 gene
Compartment Confidence
nucleus 3
extracellular 2
cytoskeleton 1
cytosol 1
plasma membrane 0
mitochondrion 0
peroxisome 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PHYHD1 Gene

Pathways & Interactions for PHYHD1 Gene

PathCards logo

SuperPathways for PHYHD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHYHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PHYHD1: view

No data available for Pathways by source and SIGNOR curated interactions for PHYHD1 Gene

Drugs & Compounds for PHYHD1 Gene

No Compound Related Data Available

Transcripts for PHYHD1 Gene

mRNA/cDNA for PHYHD1 Gene

6 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYHD1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for PHYHD1 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b · 14c · 14d
SP1: - - -
SP2: -
SP3: - - -
SP4: - - - - - - -
SP5: - -
SP7: - -
SP8: -
SP10: -

Relevant External Links for PHYHD1 Gene

GeneLoc Exon Structure for

Expression for PHYHD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHYHD1 Gene

Protein differential expression in normal tissues from HIPED for PHYHD1 Gene

This gene is overexpressed in Salivary gland (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHYHD1 Gene

Protein tissue co-expression partners for PHYHD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHYHD1

SOURCE GeneReport for Unigene cluster for PHYHD1 Gene:


Evidence on tissue expression from TISSUES for PHYHD1 Gene

  • Nervous system(4.6)
  • Liver(4.4)
  • Muscle(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with PHYHD1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHYHD1 Gene

Orthologs for PHYHD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PHYHD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PHYHD1 29 30
  • 99.43 (n)
(Bos Taurus)
Mammalia PHYHD1 29 30
  • 89.35 (n)
(Canis familiaris)
Mammalia PHYHD1 29 30
  • 88.09 (n)
(Rattus norvegicus)
Mammalia Phyhd1 29
  • 86.55 (n)
(Mus musculus)
Mammalia Phyhd1 29 16 30
  • 85.34 (n)
(Monodelphis domestica)
Mammalia PHYHD1 30
  • 45 (a)
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 41 (a)
-- 30
  • 40 (a)
-- 30
  • 36 (a)
-- 30
  • 35 (a)
(Gallus gallus)
Aves PHYHD1 29 30
  • 71.82 (n)
(Anolis carolinensis)
Reptilia PHYHD1 30
  • 80 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia phyhd1 29
  • 66.67 (n)
Str.16524 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.24381 29
(Danio rerio)
Actinopterygii phyhd1 29 30
  • 66.67 (n)
Dr.19735 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003514 29
  • 56.24 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG14688 29 30
  • 53.91 (n)
(Caenorhabditis elegans)
Secernentea CELE_Y105C5B.9 29
  • 55.16 (n)
Y105C5B.9 30
  • 28 (a)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G01490 29
  • 54.17 (n)
(Oryza sativa)
Liliopsida Os05g0473900 29
  • 53.66 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU04228 29
  • 49.77 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 41 (a)
CSA.10950 30
  • 9 (a)
Species where no ortholog for PHYHD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PHYHD1 Gene

Gene Tree for PHYHD1 (if available)
Gene Tree for PHYHD1 (if available)
Evolutionary constrained regions (ECRs) for PHYHD1: view image
Alliance of Genome Resources:
Additional Orthologs for PHYHD1

Paralogs for PHYHD1 Gene

No data available for Paralogs for PHYHD1 Gene

Variants for PHYHD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHYHD1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs10988159 -- p.Arg222Trp

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PHYHD1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PHYHD1 Gene

Variant ID Type Subtype PubMed ID
dgv12888n54 CNV loss 21841781
dgv12889n54 CNV loss 21841781
dgv4145n106 CNV deletion 24896259
esv24543 CNV gain+loss 19812545
esv2666597 CNV deletion 23128226
esv2675681 CNV deletion 23128226
esv2739077 CNV deletion 23290073
esv2739078 CNV deletion 23290073
esv3545498 CNV deletion 23714750
esv3545499 CNV deletion 23714750
esv3621821 CNV loss 21293372
esv5212 CNV loss 18987735
nsv1075680 CNV deletion 25765185
nsv1136021 CNV deletion 24896259
nsv416190 CNV deletion 16902084
nsv511415 CNV loss 21212237
nsv512120 CNV loss 21212237
nsv820766 CNV deletion 20802225
nsv825107 CNV loss 20364138

Variation tolerance for PHYHD1 Gene

Residual Variation Intolerance Score: 87.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.12; 90.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHYHD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHYHD1 Gene

Disorders for PHYHD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PHYHD1 Gene - From: COP

Disorder Aliases PubMed IDs
ehlers-danlos syndrome, hypermobility type
  • edshmb
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PHYHD1

genes like me logo Genes that share disorders with PHYHD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHYHD1 Gene

Publications for PHYHD1 Gene

  1. Crystal structure of PHYHD1A, a 2OG oxygenase related to phytanoyl-CoA hydroxylase. (PMID: 21530488) Zhang Z … McDonough MA (Biochemical and biophysical research communications 2011) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  4. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4
  5. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. (PMID: 21244100) Virok DP … Fülöp L (Journal of proteome research 2011) 3

Products for PHYHD1 Gene

Sources for PHYHD1 Gene