Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	11212
Gene name	Pyridoxal phosphate binding protein
Gene symbol	PLPBP
Synonyms (NCBI Gene)	EPEO1EPVB6DPROSC
Chromosome	8
Chromosome location	8p11.23
Summary	This gene encodes a pyridoxal 5`-phosphate binding protein involved in the homeostatic regulation of intracellular pyridoxal 5`-phosphate. This gene has a tumor suppressive effect on hepatocellular carcinoma and other solid tumors of epithelial origin. Na

Show/Hide all (7)

SNP ID	Visualize variation	Clinical significance	Consequence
rs752753379	T>C	Pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs755595256	GACA>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant
rs755946598	C>T	Pathogenic	Missense variant, coding sequence variant
rs760609867	G>A	Pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs767795673	G>A,T	Pathogenic	Splice donor variant
rs1057519273	C>G	Pathogenic	Coding sequence variant, stop gained
rs1057519424	A>G	Pathogenic	Genic downstream transcript variant, splice acceptor variant

Show/Hide all (31)

miRTarBase ID	miRNA	Experiments	Reference
MIRT574063	hsa-miR-32-3p	PAR-CLIP	20371350
MIRT574061	hsa-miR-2278	PAR-CLIP	20371350
MIRT574062	hsa-miR-15a-5p	PAR-CLIP	20371350
MIRT574060	hsa-miR-15b-5p	PAR-CLIP	20371350
MIRT574059	hsa-miR-16-5p	PAR-CLIP	20371350
MIRT574058	hsa-miR-195-5p	PAR-CLIP	20371350
MIRT574057	hsa-miR-424-5p	PAR-CLIP	20371350
MIRT574056	hsa-miR-497-5p	PAR-CLIP	20371350
MIRT574055	hsa-miR-6838-5p	PAR-CLIP	20371350
MIRT574054	hsa-miR-6501-3p	PAR-CLIP	20371350
MIRT574053	hsa-miR-520a-5p	PAR-CLIP	20371350
MIRT574052	hsa-miR-525-5p	PAR-CLIP	20371350
MIRT574051	hsa-miR-7702	PAR-CLIP	20371350
MIRT574050	hsa-miR-3180-5p	PAR-CLIP	20371350
MIRT521649	hsa-miR-302f	PAR-CLIP	23446348
MIRT521648	hsa-miR-4438	PAR-CLIP	23446348
MIRT521647	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT521646	hsa-miR-186-3p	PAR-CLIP	23446348
MIRT521645	hsa-miR-150-5p	PAR-CLIP	23446348
MIRT521644	hsa-miR-532-3p	PAR-CLIP	23446348
MIRT521643	hsa-miR-2116-3p	PAR-CLIP	23446348
MIRT521642	hsa-miR-619-5p	PAR-CLIP	23446348
MIRT521641	hsa-miR-6506-5p	PAR-CLIP	23446348
MIRT521640	hsa-miR-5702	PAR-CLIP	23446348
MIRT521638	hsa-miR-4731-5p	PAR-CLIP	23446348
MIRT521639	hsa-miR-5589-5p	PAR-CLIP	23446348
MIRT521637	hsa-miR-5095	PAR-CLIP	23446348
MIRT521635	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT521636	hsa-miR-4713-5p	PAR-CLIP	23446348
MIRT521634	hsa-miR-937-5p	PAR-CLIP	23446348
MIRT521633	hsa-miR-5089-5p	PAR-CLIP	23446348

Show/Hide all (7)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	NAS	10496079
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005829	Component	Cytosol	IDA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0042816	Process	Vitamin B6 metabolic process	IBA

MIM	HGNC	e!Ensembl
604436	9457	ENSG00000147471

O94903

Protein name

Pyridoxal phosphate homeostasis protein (PLP homeostasis protein) (Proline synthase co-transcribed bacterial homolog protein) (Pyridoxal phosphate-binding protein)

Protein function

Pyridoxal 5'-phosphate (PLP)-binding protein, which may be involved in intracellular homeostatic regulation of pyridoxal 5'-phosphate (PLP), the active form of vitamin B6.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01168	Ala_racemase_N	15 → 251	Alanine racemase, N-terminal domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous.

Sequence

MWRAGSMSAELGVGCALRAVNERVQQAVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGH
GQRTFGENYVQELLEKASNPKILSLCPEIKWHFIGHLQKQNVNKLMAVPNLFMLETVDSV
KLADKVNSSWQRKGSPERLKVMVQINTSGEESKHGLPPSETIAIVEHINAKCPNLEFVGL
MTIGSFGHDLSQGPNPDFQLLLSLREELCKKLNIPADQVELSMGMSADFQHAVEVGSTNV
RIGSTIFGERDYSKKPTPDKCAADVKAPLEVAQEH

Sequence length

275

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Epilepsy, early-onset, vitamin B6-dependent	Pathogenic; Likely pathogenic	rs2129775201, rs767795673, rs1248896048, rs1563326405, rs1057519273, rs752753379, rs1057519424, rs755946598, rs760609867, rs755595256	RCV001784882 RCV002472185 RCV002470339 RCV003154318 RCV000415554 View all (6 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
EPILEPSY, EARLY-ONSET, 1, VITAMIN B6-DEPENDENT	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PYRIDOXINE-DEPENDENT	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PLPBP-related disorder	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PYRIDOXINE-DEPENDENT-DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (24)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Aromatic amino acid decarboxylase deficiency	Aromatic amino acid decarboxylase deficiency	BEFREE	30668673		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Deficiency of aromatic-L-amino-acid decarboxylase	Deficiency Of Aromatic-L-Amino-Acid Decarboxylase	BEFREE	30668673		★★★★★ ★☆☆☆☆ Found in Text Mining only
Deficiency of glutamate decarboxylase	Deficiency Of Glutamate Decarboxylase	ORPHANET_DG	27912044		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	27912044, 28914444, 29689137, 30668673		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	27912044, 28914444	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
EPILEPSY, EARLY-ONSET, VITAMIN B6-DEPENDENT	Epilepsy	GENOMICS_ENGLAND_DG	27912044		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
EPILEPSY, EARLY-ONSET, VITAMIN B6-DEPENDENT	Epilepsy	UNIPROT_DG	27912044		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
EPILEPSY, EARLY-ONSET, VITAMIN B6-DEPENDENT	Epilepsy	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
EPILEPSY, PYRIDOXINE-DEPENDENT	Epilepsy	BEFREE	27912044		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PYRIDOXINE-DEPENDENT	Epilepsy	ORPHANET_DG	27912044		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EPILEPSY, PYRIDOXINE-DEPENDENT	Epilepsy	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperprolinemia type 2	Hyperprolinemia	BEFREE	30671974		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypophosphatasia	Hypophosphatasia	BEFREE	30671974		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial encephalopathy	Mitochondrial encephalopathy	BEFREE	30668673		★★★★★ ★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	BEFREE	30668673		★★★★★ ★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pyridoxine dependent epilepsy	Pyridoxine dependent epilepsy	Pubtator	28779752	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pyridoxine-dependent epilepsy	Pyridoxine-Dependent Epilepsy	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Speech Disorders	Speech Disorders	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Status Epilepticus	Status Epilepticus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

PLPBP (pyridoxal phosphate binding protein)