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

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; AllianceGenome:HGNC:30260
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: mouse all
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Genomic context

Location:: 17q21.32

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (47941571..47949308)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (48803361..48811099)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (46018937..46026674)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain.
Title: Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain.
Characterization of Novel Pathogenic Variants Causing Pyridox(am)ine 5'-Phosphate Oxidase-Dependent Epilepsy.
Title: Characterization of Novel Pathogenic Variants Causing Pyridox(am)ine 5'-Phosphate Oxidase-Dependent Epilepsy.
Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine-5'-phosphate oxidase deficiency.
Title: Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine-5'-phosphate oxidase deficiency.
Molecular characterization of pyridoxine 5'-phosphate oxidase and its pathogenic forms associated with neonatal epileptic encephalopathy.
Title: Molecular characterization of pyridoxine 5'-phosphate oxidase and its pathogenic forms associated with neonatal epileptic encephalopathy.
results reveal the biological function and a regulatory mechanism of PNPO, in which the MALAT1/miR-216b-5p/PNPO axis may be important in breast invasive ductal carcinoma development
Title: Pyridoxine 5'-phosphate oxidase is correlated with human breast invasive ductal carcinoma development.
TGF-beta1-mediated PNPO expression was at least in part through the upregulation of miR-143-3p in epithelial ovarian cancer.
Title: Pyridoxine 5'-phosphate oxidase is a novel therapeutic target and regulated by the TGF-β signalling pathway in epithelial ovarian cancer.
data support a pathogenic role of the c.347G>A (p.Arg116Gln) mutation in PNPO deficiency; the later onset of symptoms and the milder epilepsy phenotype of these expand the disease phenotype
Title: Pyridoxine-5'-phosphate oxidase (Pnpo) deficiency: Clinical and biochemical alterations associated with the C.347g>A (P.·Arg116gln) mutation.
Exome sequencing revealed that the patient was compound heterozygous for pathogenic mutations [c.546+1G>A (IVS5+1 G>A) and c.620delG (p.G207VfsX215)] in the PNPO gene.
Title: Pyridoxal 5ꞌ-phosphate-responsive epilepsy with novel mutations in the PNPO gene: a case report.
One sequence variant, R116Q, a single nucleotide polymorphism that has been reported in the general population, was found to have an effect on PNPO activity.
Title: Epilepsy due to PNPO mutations: genotype, environment and treatment affect presentation and outcome.
Challenge to the paradigm of exclusive PLP responsiveness in patients with pyridoxal 5'-phosphate oxidase deficiency and underlines the importance of consecutive testing of pyridoxine and PLP in neonates with antiepileptic drug-resistant seizures.
Title: Pyridoxine responsiveness in novel mutations of the PNPO gene.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Pyridoxal phosphate-responsive seizures MedGen: C1864723 OMIM: 610090 GeneReviews: PNPO Deficiency	Compare labs

EBI GWAS Catalog

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

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S2044 (e-PCR)
- UniSTS:15373

D17S1785 (e-PCR), detects polymorphism
- UniSTS:43042

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

STS-AA005137 (e-PCR)
- UniSTS:32348

STS-AA005137 (e-PCR)
- UniSTS:53089

D1S1423 (e-PCR)
- UniSTS:149619

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables FMN binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables pyridoxal phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables pyridoxamine phosphate oxidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables pyridoxamine phosphate oxidase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in pyridoxal phosphate biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in pyridoxal phosphate biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in pyridoxamine metabolic process	IEA Inferred from Electronic Annotation more info
involved_in pyridoxine biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrion	HTP more info	PubMed

General protein information

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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

EC 1.4.3.5

NCBI Reference Sequences (RefSeq)

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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.