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PNPO pyridoxamine 5'-phosphate oxidase [ Homo sapiens (human) ]

Gene ID: 55163, updated on 9-Dec-2018

Summary

Official Symbol
PNPOprovided by HGNC
Official Full Name
pyridoxamine 5'-phosphate oxidaseprovided by HGNC
Primary source
HGNC:HGNC:30260
See related
Ensembl:ENSG00000108439 MIM:603287
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDXPO; HEL-S-302
Summary
The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in liver (RPKM 22.0), kidney (RPKM 16.0) and 23 other tissues See more
Orthologs

Genomic context

See PNPO in Genome Data Viewer
Location:
17q21.32
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (47941523..47949308)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46018889..46026674)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724532 Neighboring gene SP2 antisense RNA 1 Neighboring gene Sp2 transcription factor Neighboring gene proline rich 15 like Neighboring gene CDK5 regulatory subunit associated protein 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Pyridoxal 5'-phosphate-dependent epilepsy
MedGen: C1864723 OMIM: 610090 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10535

Gene Ontology Provided by GOA

Function Evidence Code Pubs
FMN binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxamine-phosphate oxidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxamine-phosphate oxidase activity IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxamine-phosphate oxidase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
pyridoxal phosphate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxal phosphate biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
vitamin B6 metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
pyridoxine-5'-phosphate oxidase
Names
epididymis secretory protein Li 302
epididymis secretory sperm binding protein
pyridoxal 5'-phosphate synthase
pyridoxamine-phosphate oxidase
pyridoxine 5'-phosphate oxidase
NP_060599.1
XP_005257557.1
XP_011523270.1
XP_016880302.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008744.1 RefSeqGene

    Range
    5001..12786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018129.3NP_060599.1  pyridoxine-5'-phosphate oxidase

    See identical proteins and their annotated locations for NP_060599.1

    Status: REVIEWED

    Source sequence(s)
    AC018521, AK001397, BC006525, CB853441, DB228906
    Consensus CDS
    CCDS11522.1
    UniProtKB/Swiss-Prot
    Q9NVS9
    UniProtKB/TrEMBL
    V9HW45
    Related
    ENSP00000493302.1, ENST00000642017.1
    Conserved Domains (1) summary
    TIGR00558
    Location:57261
    pdxH; pyridoxamine-phosphate oxidase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    47941523..47949308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024813.1XP_016880302.1  pyridoxine-5'-phosphate oxidase isoform X1

    Related
    ENSP00000463919.2, ENST00000583599.6
    Conserved Domains (2) summary
    pfam01243
    Location:173
    Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
    pfam10590
    Location:126181
    PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
  2. XM_005257500.3XP_005257557.1  pyridoxine-5'-phosphate oxidase isoform X1

    See identical proteins and their annotated locations for XP_005257557.1

    Conserved Domains (2) summary
    pfam01243
    Location:173
    Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
    pfam10590
    Location:126181
    PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
  3. XM_011524968.2XP_011523270.1  pyridoxine-5'-phosphate oxidase isoform X2

    See identical proteins and their annotated locations for XP_011523270.1

    UniProtKB/Swiss-Prot
    Q9NVS9
    Conserved Domains (2) summary
    pfam01243
    Location:158
    Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
    pfam10590
    Location:111166
    PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
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