PLPBP

pyridoxal phosphate binding protein

Basic information

Region (hg38): 8:37762595-37779768

Previous symbols: [ "PROSC" ]

Links

ENSG00000147471

∙ NCBI:11212 ∙ OMIM:604436 ∙ HGNC:9457 ∙ Uniprot:O94903 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

pyridoxine-dependent epilepsy (Supportive), mode of inheritance: AR
epilepsy, early-onset, vitamin B6-dependent (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, early-onset 1, vitamin B6-dependent	AR	Neurologic	The condition involves neonatal or early-onset seizures, and medical treatment (with activated vitamin B6 and/or pyridoxine) has been reported as beneficial related to seizure control	Neurologic	27912044

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLPBP gene.

not_provided (234 variants)
Inborn_genetic_diseases (34 variants)
Epilepsy,_early-onset,_vitamin_B6-dependent (32 variants)
PLPBP-related_disorder (5 variants)
not_specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPBP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007198.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	62 clinvar	2 clinvar	67
missense	1 clinvar	7 clinvar	96 clinvar	6 clinvar		110
nonsense	5 clinvar	2 clinvar				7
start loss			1			1
frameshift	6 clinvar		2 clinvar			8
splice donor/acceptor (+/-2bp)	4 clinvar	1 clinvar				5
Total	16	10	102	68	2

Highest pathogenic variant AF is 0.00020784

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPBP	protein_coding	protein_coding	ENST00000328195	8	17173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0397	0.954	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.981	125	160	0.782	0.00000886	1784
Missense in Polyphen		36	49.077	0.73354		536
Synonymous	-0.381	68	64.1	1.06	0.00000388	528
Loss of Function	2.41	5	15.1	0.331	8.26e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000640
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: 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. {ECO:0000255|HAMAP-Rule:MF_03225, ECO:0000269|PubMed:27912044}.;
Disease: DISEASE: Epilepsy, early-onset, vitamin B6-dependent (EPVB6D) [MIM:617290]: An autosomal recessive neurologic disorder characterized by seizures responsive to treatment with activated vitamin B6 and/or pyridoxine. Most patients show delayed psychomotor development, mental retardation and learning disability. Seizures onset is in the first days or months of life. {ECO:0000269|PubMed:27912044}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.192

Intolerance Scores

loftool
rvis_EVS: -0.16
rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

pHI: 0.0737
hipred: Y
hipred_score: 0.543
ghis: 0.568

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Plpbp
Phenotype

Gene ontology

Biological process: biological_process
Cellular component: cytoplasm
Molecular function: pyridoxal phosphate binding