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S100PBP (S100P binding protein)

Written2012-07Kate E Lines, Tatjana Crnogorac-Jurcevic
Barts Cancer Institute, Queen Mary University of London, London, UK

(Note : for Links provided by Atlas : click)


Alias (NCBI)S100PBPR
HGNC (Hugo) S100PBP
HGNC Alias symbFLJ12903
HGNC Alias nameS100P binding protein 1
LocusID (NCBI) 64766
Atlas_Id 44308
Location 1p35.1  [Link to chromosome band 1p35]
Location_base_pair Starts at 32817653 and ends at 32858875 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping S100PBP.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)


Description There are two different transcript variants of S100PBP. Variant 1 is 4317 base pairs and contains 7 exons. Variant 2 is 1483 base pairs and also contains 7 exons. This is shown in the above alignment. The coding sequence for each isoform is indicated in red, with the non-coding sequence in grey. Unmatched base pairs between the two isoforms are highlighted in green and the position of a missing CAG codon in isoform B is circled. The end of the isoform B sequence is indicated by a bold line.


Description S100PBP isoform A codes for a 45 kDa protein and isoform B for 37 kDa protein.
Secondary structure analysis of the S100PBP protein sequence was performed using the secondary structure consensus prediction tool (NPS@, Lyon, France). Based on three different methods: DSC (Discrimination of protein Secondary structure Class), MLRC (Multivariate Linear Regression Combination) and PHD neural network system, S100PBP was shown to be largely unstructured and unfolded, as seen above ("h" represents a helix, "c" a coil and "e" an extended strand).
Expression S100PBP is expressed in various normal tissues including prostate and lung and in both the endocrine and exocrine pancreas. S100PBP is also expressed in malignant tissues such as liver hepatocellular carcinoma and thyroid carcinoma (Lines et al., 2012).
In pancreas, S100PBP is expressed in decreasing levels as cancer develops and progresses, which is an inverse pattern of expression of its binding partner, S100P. This is shown on picture below (a= acinar cells, d= ducts; PanIN= pancreatic intraepithelial neoplasia, a precursor lesion to pancreatic cancer, black arrows= PanIN-1, red arrows= PanIN-2; PDAC= pancreatic cancer).
Localisation Predominantly nuclear.
Function The exact functions of S100PBP are currently unknown, however it has been shown that S100PBP can bind to the metastasis related protein S100P (Dowen et al., 2005).
Homology No homology to any currently described protein is seen.


Note No mutations have yet been reported.

Implicated in

Entity Pancreatic ductal adenocarcinoma (PDAC)
Note Overexpression of S100PBP in FA6 pancreatic cancer cells that show low levels of endogenous S100PBP expression and silencing of S100PBP in MiaPaCa2 cells (high levels of endogenous S100PBP) showed no effect on proliferation or wound healing. While cell migration was not affected in majority of tested pancreatic cancer cell lines after modulation of S100PBP expression, significant changes in invasion (increase in MiaPaCa2 and Panc1 cells after S100PBP silencing and decrease in RwP1 cells after overexpression) were seen. However, the most affected cellular function after modulation of S100PBP expression was adhesion. Loss of S100PBP causes an increase in pancreatic cancer cell adhesion to extracellular matrix proteins which was mediated by cysteine protease Cathepsin Z (CTSZ) and the integrin ανβ5 (Lines et al., 2012).
Schematic and simplified diagram of the putative mechanism behind S100PBP mediated changes in pancreatic cell adhesion is shown below: in normal cells where S100PBP is highly expressed, low levels of CTSZ are present; no or very little ανβ5 is seen on the cellular surface. In cancer cells (PDAC), S100PBP levels decrease, which results in an increase in CTSZ expression; CTSZ is then secreted and can interact with ανβ5, promoting thus the adhesion.
Disease Pancreatic cancer.


Expression of S100P and its novel binding partner S100PBPR in early pancreatic cancer.
Dowen SE, Crnogorac-Jurcevic T, Gangeswaran R, Hansen M, Eloranta JJ, Bhakta V, Brentnall TA, Luttges J, Kloppel G, Lemoine NR.
Am J Pathol. 2005 Jan;166(1):81-92.
PMID 15632002
S100P-binding protein, S100PBP, mediates adhesion through regulation of cathepsin Z in pancreatic cancer cells.
Lines KE, Chelala C, Dmitrovic B, Wijesuriya N, Kocher HM, Marshall JF, Crnogorac-Jurcevic T.
Am J Pathol. 2012 Apr;180(4):1485-94. Epub 2012 Feb 11.
PMID 22330678


This paper should be referenced as such :
Lines, KE ; Crnogorac-Jurcevic, T
S100PBP (S100P binding protein)
Atlas Genet Cytogenet Oncol Haematol. 2013;17(1):40-44.
Free journal version : [ pdf ]   [ DOI ]

External links

HGNC (Hugo)S100PBP   25768
Entrez_Gene (NCBI)S100PBP    S100P binding protein
GeneCards (Weizmann)S100PBP
Ensembl hg19 (Hinxton)ENSG00000116497 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000116497 [Gene_View]  ENSG00000116497 [Sequence]  chr1:32817653-32858875 [Contig_View]  S100PBP [Vega]
ICGC DataPortalENSG00000116497
TCGA cBioPortalS100PBP
AceView (NCBI)S100PBP
Genatlas (Paris)S100PBP
SOURCE (Princeton)S100PBP
Genetics Home Reference (NIH)S100PBP
Genomic and cartography
GoldenPath hg38 (UCSC)S100PBP  -     chr1:32817653-32858875 +  1p35.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)S100PBP  -     1p35.1   [Description]    (hg19-Feb_2009)
GoldenPathS100PBP - 1p35.1 [CytoView hg19]  S100PBP - 1p35.1 [CytoView hg38]
genome Data Viewer NCBIS100PBP [Mapview hg19]  
Gene and transcription
Genbank (Entrez)AA557330 AK022965 AK025811 AK090711 BC015175
RefSeq transcript (Entrez)NM_001017406 NM_001256121 NM_022753
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)S100PBP
Alternative Splicing GalleryENSG00000116497
Gene ExpressionS100PBP [ NCBI-GEO ]   S100PBP [ EBI - ARRAY_EXPRESS ]   S100PBP [ SEEK ]   S100PBP [ MEM ]
Gene Expression Viewer (FireBrowse)S100PBP [ Firebrowse - Broad ]
GenevisibleExpression of S100PBP in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)64766
GTEX Portal (Tissue expression)S100PBP
Human Protein AtlasENSG00000116497-S100PBP [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96BU1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96BU1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96BU1
Splice isoforms : SwissVarQ96BU1
Domains : Interpro (EBI)S100PBP   
Domain families : Pfam (Sanger)S100PBPR (PF15427)   
Domain families : Pfam (NCBI)pfam15427   
Conserved Domain (NCBI)S100PBP
Blocks (Seattle)S100PBP
Human Protein Atlas [tissue]ENSG00000116497-S100PBP [tissue]
Peptide AtlasQ96BU1
IPIIPI00009366   IPI00555742   IPI00977758   IPI00975901   IPI01015822   IPI00978992   IPI00980751   IPI00985468   IPI00980158   
Protein Interaction databases
IntAct (EBI)Q96BU1
Ontologies - Pathways
Ontology : AmiGOprotein binding  nucleus  nucleus  cytosol  cytosol  nuclear speck  calcium-dependent protein binding  calcium-dependent protein binding  
Ontology : EGO-EBIprotein binding  nucleus  nucleus  cytosol  cytosol  nuclear speck  calcium-dependent protein binding  calcium-dependent protein binding  
NDEx NetworkS100PBP
Atlas of Cancer Signalling NetworkS100PBP
Wikipedia pathwaysS100PBP
Orthology - Evolution
GeneTree (enSembl)ENSG00000116497
Phylogenetic Trees/Animal Genes : TreeFamS100PBP
Homologs : HomoloGeneS100PBP
Homology/Alignments : Family Browser (UCSC)S100PBP
Gene fusions - Rearrangements
Fusion : Fusion_HubHMGCL--S100PBP    MAPKBP1--S100PBP    MAT2A--S100PBP    S100PBP--NFIA    S100PBP--PARP15    S100PBP--STS    S100PBP--YARS    S100PBP--ZBTB8A    USP6--S100PBP    YARS--S100PBP   
Fusion : QuiverS100PBP
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerS100PBP [hg38]
Exome Variant ServerS100PBP
GNOMAD BrowserENSG00000116497
Varsome BrowserS100PBP
Genomic Variants (DGV)S100PBP [DGVbeta]
DECIPHERS100PBP [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisS100PBP 
ICGC Data PortalS100PBP 
TCGA Data PortalS100PBP 
Broad Tumor PortalS100PBP
OASIS PortalS100PBP [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICS100PBP  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DS100PBP
Mutations and Diseases : HGMDS100PBP
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch S100PBP
DgiDB (Drug Gene Interaction Database)S100PBP
DoCM (Curated mutations)S100PBP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)S100PBP (select a term)
NCG6 (London) select S100PBP
Cancer3DS100PBP(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry S100PBP
NextProtQ96BU1 [Medical]
Target ValidationS100PBP
Huge Navigator S100PBP [HugePedia]
Clinical trials, drugs, therapy
Protein Interactions : CTD
Pharm GKB GenePA142670958
Clinical trialS100PBP
canSAR (ICR)S100PBP (select the gene name)
DataMed IndexS100PBP
PubMed14 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 25 20:09:27 CET 2021

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