Gene Gene information from NCBI Gene database.
Entrez ID 8566
Gene name Pyridoxal kinase
Gene symbol PDXK
Synonyms (NCBI Gene)
C21orf124C21orf97HEL-S-1aHMSN6CPKHPNKPRED79
Chromosome 21
Chromosome location 21q22.3
Summary 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. A
SNPs SNP information provided by dbSNP.
3
SNP ID Visualize variation Clinical significance Consequence
rs757480516 G>A Pathogenic Genic downstream transcript variant, missense variant, coding sequence variant
rs759333796 G>A Pathogenic Genic downstream transcript variant, missense variant, coding sequence variant
rs1601814238 T>A Pathogenic Genic downstream transcript variant, missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1230
miRTarBase ID miRNA Experiments Reference
MIRT016586 hsa-miR-193b-3p Proteomics 21512034
MIRT030630 hsa-miR-24-3p Sequencing 20371350
MIRT030630 hsa-miR-24-3p Microarray 19748357
MIRT051266 hsa-miR-16-5p CLASH 23622248
MIRT049519 hsa-miR-92a-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
38
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0000287 Function Magnesium ion binding IDA 17766369
GO:0005524 Function ATP binding IDA 16600635, 17766369
GO:0005524 Function ATP binding IEA
GO:0005576 Component Extracellular region TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
179020 8819 ENSG00000160209
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O00764
Protein name Pyridoxal kinase (EC 2.7.1.35) (Pyridoxine kinase)
Protein function Catalyzes the phosphorylation of the dietary vitamin B6 vitamers pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM) to form pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), respectively (Probabl
PDB 2AJP , 2F7K , 2YXT , 2YXU , 3FHX , 3FHY , 3KEU , 4EN4 , 4EOH , 8WR2
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08543 Phos_pyr_kin 70 284 Phosphomethylpyrimidine kinase Family
Tissue specificity TISSUE SPECIFICITY: Ubiquitous (PubMed:31187503, PubMed:9099727). Highly expressed in testis (PubMed:9099727). {ECO:0000269|PubMed:31187503, ECO:0000269|PubMed:9099727}.; TISSUE SPECIFICITY: [Isoform 3]: In adult testis and spermatozoa. {ECO:0000269|PubMe
Sequence
Sequence length 312
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Vitamin B6 metabolism
Metabolic pathways
Biosynthesis of cofactors
  Neutrophil degranulation
Vitamins B6 activation to pyridoxal phosphate
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
29
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy Pathogenic; Likely pathogenic rs757480516, rs759333796, rs1601814238 RCV000788038
RCV000788039
RCV001003348
PDXK-related disorder Pathogenic rs757480516 RCV003396366
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Familial cancer of breast Benign; Likely benign rs8128639, rs112579284 RCV005919872
RCV005930232
Gastric cancer Benign rs1079268 RCV005924892
Hepatocellular carcinoma Benign; Likely benign rs8128639, rs112579284 RCV005915476
RCV005930234
Malignant lymphoma, large B-cell, diffuse Benign rs8128639 RCV005915477
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Blindness Associate 31187503
Carcinoma Hepatocellular Associate 36750831
Carcinoma Non Small Cell Lung Associate 23343765, 26387143
Glomerulonephritis IGA Associate 35769467
Glucocorticoid Receptor Deficiency Inhibit 17696614
Inflammatory Bowel Diseases Associate 35769467
Optic Atrophy Associate 31187503
Ovarian Neoplasms Associate 31973910
Parkinson Disease Associate 20035503
Peripheral Nervous System Diseases Associate 31187503