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Aliases for PDXK Gene

Aliases for PDXK Gene

  • Pyridoxal Kinase 2 3 3 5
  • Pyridoxal (Pyridoxine, Vitamin B6) Kinase 2 3
  • Pyridoxine Kinase 3 4
  • C21orf124 3 4
  • C21orf97 3 4
  • PKH 3 4
  • PNK 3 4
  • Epididymis Secretory Sperm Binding Protein Li 1a 3
  • Chromosome 21 Open Reading Frame 124 2
  • Chromosome 21 Open Reading Frame 97 2
  • Pyridoxamine Kinase 3
  • Vitamin B6 Kinase 3
  • EC 2.7.1.35 4
  • HEL-S-1a 3
  • PRED79 3

External Ids for PDXK Gene

Previous HGNC Symbols for PDXK Gene

  • C21orf97
  • C21orf124

Previous GeneCards Identifiers for PDXK Gene

  • GC21P041648
  • GC21P043996
  • GC21P043997
  • GC21P043998
  • GC21P043964
  • GC21P043965
  • GC21P045138
  • GC21P030506

Summaries for PDXK Gene

Entrez Gene Summary for PDXK Gene

  • The protein encoded by this gene phosphorylates vitamin B6, a step required for the conversion of vitamin B6 to pyridoxal-5-phosphate, an important cofactor in intermediary metabolism. The encoded protein is cytoplasmic and probably acts as a homodimer. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PDXK Gene

PDXK (Pyridoxal Kinase) is a Protein Coding gene. Diseases associated with PDXK include Bartter Syndrome, Type 3. Among its related pathways are Metabolism and Vitamin B6 metabolism. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and pyridoxal phosphate binding.

UniProtKB/Swiss-Prot for PDXK Gene

  • Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Gene Wiki entry for PDXK Gene

Additional gene information for PDXK Gene

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

Genomics for PDXK Gene

GeneHancer (GH) Regulatory Elements for PDXK Gene

Promoters and enhancers for PDXK Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH21J043724 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 661.4 +13.8 13805 17.4 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PDXK WDR4 RRP1B U2AF1 PWP2 ENSG00000233754 HSF2BP ENSG00000184441 TRPM2 SIK1
GH21J043718 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 659.2 +1.4 1362 4.5 HDGF ARID4B SIN3A DMAP1 ZBTB7B IRF4 YY1 ZNF207 ZNF143 FOS PDXK ENSG00000184441 WDR4 PKNOX1 RRP1B PWP2 U2AF1 C21orf2 H2BFS LOC105372824
GH21J043643 Enhancer 1.5 FANTOM5 Ensembl ENCODE 22.3 -73.4 -73426 3.4 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 SLC30A9 PDXK WDR4 SIK1 RRP1B PWP2 FRGCA U2AF1 ENSG00000233754 HSF2BP MIR6070
GH21J043658 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 13.7 -58.9 -58921 2.8 HDGF SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 POLR2B RRP1B HSF2BP PWP2 WDR4 U2AF1 ENSG00000184441 ENSG00000233754 PKNOX1 TRAPPC10 PDXK
GH21J043509 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 14.8 -202.5 -202483 14.1 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B NEUROD1 FEZF1 DMAP1 ZBTB7B PDXK HSF2BP WDR4 U2AF1 ENSG00000233754 SIK1 RPL31P1 PIR54224
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDXK on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDXK gene promoter:
  • c-Jun
  • ATF-2
  • AP-1
  • HEN1
  • HNF-1
  • HNF-1A
  • Arnt
  • Sox9
  • Max1
  • c-Myc

Genomic Locations for PDXK Gene

Genomic Locations for PDXK Gene
chr21:43,719,094-43,762,307
(GRCh38/hg38)
Size:
43,214 bases
Orientation:
Plus strand
chr21:45,138,975-45,182,188
(GRCh37/hg19)
Size:
43,214 bases
Orientation:
Plus strand

Genomic View for PDXK Gene

Genes around PDXK on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDXK Gene

Proteins for PDXK Gene

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

    Protein Symbol:
    O00764-PDXK_HUMAN
    Recommended name:
    Pyridoxal kinase
    Protein Accession:
    O00764
    Secondary Accessions:
    • Q7Z2Y0
    • Q9BS02

    Protein attributes for PDXK Gene

    Size:
    312 amino acids
    Molecular mass:
    35102 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDXK Gene

    Alternative splice isoforms for PDXK Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDXK Gene

Post-translational modifications for PDXK Gene

  • Ubiquitination at Lys275, Lys139, and isoforms=76
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PDXK Gene

Domains & Families for PDXK Gene

Gene Families for PDXK Gene

Human Protein Atlas (HPA):
  • Enzymes
  • FDA approved drug targets
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PDXK Gene

Suggested Antigen Peptide Sequences for PDXK Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O00764

UniProtKB/Swiss-Prot:

PDXK_HUMAN :
  • Belongs to the pyridoxine kinase family.
Family:
  • Belongs to the pyridoxine kinase family.
genes like me logo Genes that share domains with PDXK: view

Function for PDXK Gene

Molecular function for PDXK Gene

UniProtKB/Swiss-Prot Function:
Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + pyridoxal = ADP + pyridoxal 5-phosphate.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 5.5-6.0.;
GENATLAS Biochemistry:
pyridoxal kinase,ubiquitously expressed,repressed by ligands of the benzodiazepine receptor

Enzyme Numbers (IUBMB) for PDXK Gene

Phenotypes From GWAS Catalog for PDXK Gene

Gene Ontology (GO) - Molecular Function for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 17766369
GO:0005524 ATP binding IDA,IEA 16600635
GO:0008270 zinc ion binding IDA 10987144
GO:0008478 pyridoxal kinase activity IEA,TAS --
GO:0016301 kinase activity IEA --
genes like me logo Genes that share ontologies with PDXK: view
genes like me logo Genes that share phenotypes with PDXK: view

Animal Models for PDXK Gene

MGI Knock Outs for PDXK:
  • Pdxk Pdxk<tm1a(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for PDXK

Clone Products

  • Addgene plasmids for PDXK

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDXK Gene

Localization for PDXK Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDXK Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 PDXK gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
plasma membrane 2
cytoskeleton 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005634 nucleus HDA 21630459
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PDXK: view

Pathways & Interactions for PDXK Gene

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

Pathways by source for PDXK Gene

Gene Ontology (GO) - Biological Process for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008283 cell proliferation IDA 10930737
GO:0009443 pyridoxal 5-phosphate salvage IBA,IEA --
GO:0016310 phosphorylation IEA --
GO:0042816 vitamin B6 metabolic process TAS --
GO:0042823 pyridoxal phosphate biosynthetic process IDA 9099727
genes like me logo Genes that share ontologies with PDXK: view

No data available for SIGNOR curated interactions for PDXK Gene

Drugs & Compounds for PDXK Gene

(15) Drugs for PDXK Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Approved Nutra Target 197
Pyridoxine Approved, Investigational, Vet_approved Nutra Target, ligand 198,198
Potassium Approved, Investigational Pharma 0
Magnesium Approved Nutra 0
Pyridoxal Phosphate Approved, Investigational Nutra 17

(6) Additional Compounds for PDXK Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with PDXK: view

Transcripts for PDXK Gene

Unigene Clusters for PDXK Gene

Pyridoxal (pyridoxine, vitamin B6) kinase:
Representative Sequences:

Clone Products

  • Addgene plasmids for PDXK

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

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^
SP1: - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - -
SP3: - -
SP4:
SP5: - - - - - - - - -
SP6: - - - - - - - - - - - - -
SP7: - - -
SP8: - -
SP9: - - -
SP10: - - - - - - - - -
SP11:
SP12: -
SP13: - - - - -

ExUns: 18a · 18b · 18c · 18d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for PDXK Gene

GeneLoc Exon Structure for
PDXK
ECgene alternative splicing isoforms for
PDXK

Expression for PDXK Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDXK Gene

This gene is overexpressed in Nasopharynx (8.6).

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



Protein tissue co-expression partners for PDXK Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDXK Gene:

PDXK

SOURCE GeneReport for Unigene cluster for PDXK Gene:

Hs.284491

mRNA Expression by UniProt/SwissProt for PDXK Gene:

O00764-PDXK_HUMAN
Tissue specificity: Ubiquitous. Isoform 3 is detected in adult testis and spermatozoa.

Evidence on tissue expression from TISSUES for PDXK Gene

  • Nervous system(4.7)
  • Liver(4.5)
  • Eye(4.3)
  • Lung(3.9)
  • Bone marrow(2.8)
  • Intestine(2.6)
  • Pancreas(2.4)
  • Kidney(2.3)
  • Muscle(2.2)
  • Blood(2.1)
  • Heart(2.1)
  • Spleen(2)
genes like me logo Genes that share expression patterns with PDXK: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDXK Gene

Orthologs for PDXK Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDXK Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDXK 34 33
  • 98.82 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PDXK 34 33
  • 86 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pdxk 16 34 33
  • 84.72 (n)
dog
(Canis familiaris)
Mammalia PDXK 34 33
  • 84.14 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdxk 33
  • 83.55 (n)
oppossum
(Monodelphis domestica)
Mammalia PDXK 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDXK 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDXK 34 33
  • 75.46 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDXK 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdxk 33
  • 70.44 (n)
zebrafish
(Danio rerio)
Actinopterygii PDXK (1 of 3) 34
  • 74 (a)
OneToMany
LOC100535341 33
  • 69.3 (n)
pdxkb 34
  • 67 (a)
OneToMany
pdxka 34
  • 65 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.60 33
fruit fly
(Drosophila melanogaster)
Insecta CG34455 34 33
  • 55.94 (n)
OneToOne
CG4446 35
  • 47 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005929 33
  • 55.37 (n)
worm
(Caenorhabditis elegans)
Secernentea F57C9.1 34 33
  • 51.13 (n)
OneToOne
F57C9.1b 35
  • 40 (a)
F57C9.1a 35
  • 39 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BUD16 36 34
  • 34 (a)
BUD17 34
  • 32 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons SOS4 33
  • 51.9 (n)
rice
(Oryza sativa)
Liliopsida Os12g0600400 33
  • 52.36 (n)
corn
(Zea mays)
Liliopsida Zm.3752 33
wheat
(Triticum aestivum)
Liliopsida Ta.27523 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8531 34
  • 59 (a)
OneToOne
Cin.4083 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4083 33
Species where no ortholog for PDXK was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for PDXK Gene

ENSEMBL:
Gene Tree for PDXK (if available)
TreeFam:
Gene Tree for PDXK (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDXK: view image

Paralogs for PDXK Gene

(2) SIMAP similar genes for PDXK Gene using alignment to 5 proteins:

  • PDXK_HUMAN
  • A8MT14_HUMAN
  • A8MV33_HUMAN
  • F2Z2Y4_HUMAN
  • G1UI32_HUMAN

Pseudogenes.org Pseudogenes for PDXK Gene

genes like me logo Genes that share paralogs with PDXK: view

No data available for Paralogs for PDXK Gene

Variants for PDXK Gene

Sequence variations from dbSNP and Humsavar for PDXK Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000000157 -- 43,741,982(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000003194 -- 43,717,222(+) G/A upstream_transcript_variant
rs1000042038 -- 43,738,696(+) G/C 3_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs1000157986 -- 43,733,535(+) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000210594 -- 43,753,154(+) G/A genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
dgv7874n54 CNV gain 21841781
dgv7875n54 CNV loss 21841781
dgv7876n54 CNV loss 21841781
dgv7877n54 CNV loss 21841781
esv1717308 CNV insertion 17803354
esv25264 CNV loss 19812545
esv2664281 CNV deletion 23128226
esv33771 CNV gain 17666407
esv33817 CNV loss 17666407
esv3557791 CNV deletion 23714750
esv3647111 CNV loss 21293372
nsv1072187 CNV deletion 25765185
nsv1150161 CNV deletion 26484159
nsv459291 CNV loss 19166990
nsv470904 CNV loss 18288195
nsv509799 CNV insertion 20534489
nsv520305 CNV loss 19592680
nsv587703 CNV loss 21841781
nsv587704 CNV loss 21841781
nsv587711 CNV loss 21841781
nsv587712 CNV loss 21841781
nsv587716 CNV loss 21841781
nsv587717 CNV loss 21841781
nsv834107 CNV loss 17160897
nsv834108 CNV loss 17160897
nsv953642 CNV deletion 24416366

Variation tolerance for PDXK Gene

Residual Variation Intolerance Score: 45.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDXK Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDXK Gene

MalaCards: The human disease database

(1) MalaCards diseases for PDXK Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
bartter syndrome, type 3
  • barts3
- elite association - COSMIC cancer census association via MalaCards
Search PDXK in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PDXK

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

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

Publications for PDXK Gene

  1. Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. (PMID: 9099727) Hanna MC … Kirkness EF (The Journal of biological chemistry 1997) 2 3 4 22 58
  2. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. (PMID: 20035503) Elstner M … Turnbull DM (Annals of neurology 2009) 3 22 44 58
  3. Human pyridoxal kinase: overexpression and properties of the recombinant enzyme. (PMID: 10987144) Lee HS … Kwon OS (Molecules and cells 2000) 3 4 22 58
  4. The PDXK rs2010795 variant is not associated with Parkinson disease in Italy. (PMID: 20373357) Guella I … Duga S (Annals of neurology 2010) 3 44 58
  5. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 44 58

Products for PDXK Gene