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    PLPBP pyridoxal phosphate binding protein [ Homo sapiens (human) ]

    Gene ID: 11212, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PLPBPprovided by HGNC
    Official Full Name
    pyridoxal phosphate binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:9457
    See related
    Ensembl:ENSG00000147471 MIM:604436; AllianceGenome:HGNC:9457
    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
    EPEO1; PROSC; EPVB6D
    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. Naturally occurring mutations in this gene are associated with a pyridoxine-dependent epilepsy. [provided by RefSeq, Mar 2017]
    Expression
    Ubiquitous expression in kidney (RPKM 12.8), colon (RPKM 10.6) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PLPBP in Genome Data Viewer
    Location:
    8p11.23
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (37762546..37779768)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38038942..38056164)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (37620064..37637286)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37594714-37595506 Neighboring gene ER lipid raft associated 2 Neighboring gene STING1 ER exit protein 1 pseudogene Neighboring gene uncharacterized LOC124901934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27229 Neighboring gene Sharpr-MPRA regulatory region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27231 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:37638448-37639647 Neighboring gene uncharacterized LOC105379381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37645266-37645774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37652831-37653396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37653397-37653962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19109 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27233 Neighboring gene adhesion G protein-coupled receptor A2 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37667034-37667256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37671601-37672366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37672367-37673132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37673133-37673898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37679325-37679898 Neighboring gene VISTA enhancer hs1665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37685664-37686632 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37696873-37697010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37699228-37699928 Neighboring gene BRF2 general transcription factor IIIB subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. PLPBP Deficiency. Adam MP, et al. , 1993. PMID 36795901
    2. Pyridoxine supply in human development. Bowling FG. Semin Cell Dev Biol, 2011 Aug. PMID 21664474
    3. Integrative genomic identification of genes on 8p associated with hepatocellular carcinoma progression and patient survival. Roessler S, et al. Gastroenterology, 2012 Apr. PMID 22202459, Free PMC Article
    4. Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B(6)-Dependent Epilepsy. Darin N, et al. Am J Hum Genet, 2016 Dec 1. PMID 27912044, Free PMC Article
    5. Confirmation of mutations in PROSC as a novel cause of vitamin B ((6)) -dependent epilepsy. Plecko B, et al. J Med Genet, 2017 Dec. PMID 28391250

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Maintenance of cellular vitamin B6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein.
      Title: Maintenance of cellular vitamin B(6) levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein.
    2. We therefore confirm PROSC as a novel gene for vitamin-B6-dependent epilepsy and delineate a non-specific plasma vitamin B6 profile under pyridoxine treatment.
      Title: Confirmation of mutations in PROSC as a novel cause of vitamin B ((6)) -dependent epilepsy.
    3. Exploiting the universality of the Synechococcus elongatus COG0325 (PiPY) functions, it has been used in site-directed mutagenesis studies to shed light on disease causation by epilepsy-associated mutations in the human COG0325 gene PROSC.
      Title: Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B(6) -dependent epilepsy.
    4. studies suggest that PROSC is involved in intracellular homeostatic regulation of pyridoxal 5'-phosphate, supplying this cofactor to apoenzymes while minimizing any toxic side reactions
      Title: Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B(6)-Dependent Epilepsy.
    Submit: New GeneRIF Correction

    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
    Epilepsy, early-onset, vitamin B6-dependent
    MedGen: C4310632 OMIM: 617290 GeneReviews: PLPBP Deficiency
    		not available

    EBI GWAS Catalog

    Description
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11861

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables pyridoxal phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in vitamin B6 metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    pyridoxal phosphate homeostasis protein
    Names
    PLP homeostasis protein
    proline synthase co-transcribed bacterial homolog protein
    proline synthetase co-transcribed bacterial homolog protein

    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.

    Genomic

    1. NG_053030.1 RefSeqGene

      Range
      5893..23016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001349346.2 → NP_001336275.1  pyridoxal phosphate homeostasis protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC138356, AL136616, BC012334, BM984988
      UniProtKB/TrEMBL
      A8K520
      Conserved Domains (1) summary
      cd06822
      Location:17 → 258
      PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

    2. NM_001349347.2 → NP_001336276.1  pyridoxal phosphate homeostasis protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC138356, BM984988
      UniProtKB/TrEMBL
      A8K520
      Conserved Domains (1) summary
      cd06822
      Location:17 → 246
      PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

    3. NM_001349348.2 → NP_001336277.1  pyridoxal phosphate homeostasis protein isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses a downstream start codon compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to variant 1.
      Source sequence(s)
      AC138356, BM984988
      UniProtKB/TrEMBL
      B3KMP6
      Conserved Domains (1) summary
      cd06822
      Location:1 → 196
      PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

    4. NM_001349349.1 → NP_001336278.1  pyridoxal phosphate homeostasis protein isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks a portion of the 3' coding region and differs in the 3' UTR compared to variant 1. The encoded protein has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AA463397, AC138356
      Conserved Domains (1) summary
      cl00261
      Location:52 → 142
      PLPDE_III; Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes

    5. NM_007198.4 → NP_009129.1  pyridoxal phosphate homeostasis protein isoform 2

      See identical proteins and their annotated locations for NP_009129.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL136616, BC012334, BM984988
      Consensus CDS
      CCDS6096.1
      UniProtKB/Swiss-Prot
      O94903, Q6FI94
      UniProtKB/TrEMBL
      A8K520
      Related
      ENSP00000333551.3, ENST00000328195.8
      Conserved Domains (1) summary
      cd06822
      Location:17 → 248
      PLPDE_III_YBL036c_euk; Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      37762546..37779768
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      38038942..38056164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94903.1 GenPept UniProtKB/Swiss-Prot:O94903

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