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S100A13 (S100 calcium binding protein A13)

Written2008-02Carlo Barone, Cinzia Bagalà, Matteo Landriscina
Catholic University of Sacred Heart, Institute of Internal Medicine, Oncology Unit, Largo A. Gemelli 8, 00168 Roma, Itlaly

(Note : for Links provided by Atlas : click)

Identity

Alias_namesS100 calcium-binding protein A13
Other alias
HGNC (Hugo) S100A13
LocusID (NCBI) 6284
Atlas_Id 44197
Location 1q21.3  [Link to chromosome band 1q21]
Location_base_pair Starts at 153591276 and ends at 153606568 bp from pter ( according to hg19-Feb_2009)  [Mapping S100A13.png]
Local_order Co-localized in a gene cluster with other S100 genes on 1q21.3.
Fusion genes
(updated 2016)
CHTOP (1q21.3) / S100A13 (1q21.3)KPNB1 (17q21.32) / S100A13 (1q21.3)S100A13 (1q21.3) / AEBP2 (12p12.3)
S100A13 (1q21.3) / ATP2B2 (3p25.3)S100A13 (1q21.3) / MAT2B (5q34)S100A13 (1q21.3) / S100A13 (1q21.3)
ZFAT (8q24.22) / S100A13 (1q21.3)

DNA/RNA

Description The gene contains five exons and four introns; it is composed of a variable 5' untranslated region, a 296 bp coding sequence, a 3' untranslated region and a polyA tail.
Transcription The gene has 5 alternatively spliced variants encoding the same protein; the variant 1 represents the longest transcript (951 bp), all the other variants have distinct and shorter 5'UTR as compared to variant 1.

Protein

 
  Schematic representation of the domains structure of S100A13 monomer.
Description Small homodimeric protein (98 amino-acids, M.W. 11,47 kDa), with 2 Ca2+-binding EF-hands motifs and a positively charged C-terminal region mediating the interaction with specific target molecules.
Expression Highly expressed in skeletal muscle, heart, kidney, pancreas, ovary, spleen and small intestine, follicle cells of thyroid; moderate expression in prostate, testis, colon and brain; little expression in thymus, lung, liver and placenta, non detectable expression in leukocytes.
Localisation Cytosolic
Function It may function in exocytosis, since it is one of the targets of some antiallergic drugs, such as amlexanox and cromolyn, which inhibit degranulation of mast cells; marker of active angiogenesis in some tumours and endometriosis; released with signal peptide-less proteins such as FGF1 and IL-1alpha upon intracellular stress conditions.
Homology 68% homology with human S100A14 and 50.5% with human S100A5; 86,7% with mouse S100A13.

Implicated in

Note
  
Entity Astrocytic gliomas
Disease Astrocytic gliomas are the most common primary brain tumours; they include WHO grade IV tumours, such as glioblastomas with its variants and WHO grade III tumours (anaplastic forms of astrocytoma, oligodendroglioma and oligoastrocytoma).
Prognosis Poor for glioblastoma, relatively better for who grade III tumours.
Cytogenetics Anaplastic astrocytomas carry gain of chromosome 7 or 7q and deletions on chromosomes 6, 9p, 11p, 19q and 22q. Glioblastomas demonstrate deletions of chromosome 10 and allelic losses on 19q and 13q.
Oncogenesis Homozigous deletion of CDKN2A, CDKN2B and p14ARF(9p) (9p), negative regulators of cell cycle or amplification of the cyclin-dependent kinase CDK4 are frequent in astrocytoma gr. III and glioblastoma. Glioblastoma and a subset of anaplastic astrocytoma with no abnormality of CDK4 and CDKN2A carries mutation in the retinoblastoma gene (Rb1); p53-pathway is frequently altered and PTEN is mutated in 30-40% of glioblastoma and in astrocytoma with poor prognosis. Astrocytic gliomas generally stain positive for S-100 proteins; S100-A13 is up-regulated in high-grade gliomas and correlated with microvessel density and tumour grading.
  
  
Entity Endometriosis
Disease Endometriosis is characterized by the presence and proliferation of functional endometrial glands and stroma outside the uterine cavity. It is a multifactorial genetic disorders. Increasing evidence points to the role of angiogenesis in the disease pathogenesis and many angiogenic factors and cytokines such as VEGF-A, FGF1, endoglin and interleukin-1 alpha are up-regulated in endometriotic lesions. S100A13 is over-expressed in endometriotic specimens, particularly in microvascular endothelia.
Prognosis It is a chronic and recurrent disease associated with infertility.
  
  
Entity Lung cancer
Disease Lung cancer is the most preventable of all the major forms of cancer since at least 75% of all cases worldwide are due to tobacco smoking. It can be classified into two main groups: small cell lung cancer and non-small cell lung cancer. The latter group is a heterogeneous aggregate of at least 3 distinct histologies including epidermoid or squamous carcinoma, adenocarcinoma and large cell carcinoma with the potential for cure with surgical resection when localized. Small cell lung carcinoma has a greater tendency to be disseminated by the time of diagnosis but is much more responsive to chemotherapy and radiation compared to non-small cell lung cancer.
Prognosis Poor; small cell carcinoma has the most aggressive clinical course with median survival of only 2-4 months without treatment.
Cytogenetics Loss of heterozigosity in chromosome regions 3p (fragile histidine triad, FHIT, locus), 12p, 13q (Rb1 locus) and 17p (p53 locus).
Oncogenesis Inactivation of p16 by promoter hypermethylation is more frequent in squamous cell carcinoma compared with adenocarcinoma and is almost never found in small-cell lung cancer; K-ras mutations are documented only in non- small cell lung tumours particularly adenocarcinoma. Overexpression of myc family members and inactivation of p53, pRb and FHIT are found in all histologic types of lung cancer. S100P and S100A2 may be predictors of distant metastasis and poor survival in non-small cell lung tumours since they are overexpressed in tumours that metastatized during the course of the disease; S100A13 expression correlates with a more invasive phenotype in vitro.
  

Bibliography

Endoglin (cd105) and S100A13 as markers of active angiogenesis in endometriosis.
Hayrabedyan S, Kyurkchiev S, Kehayov I
Reproductive biology. 2005 ; 5 (1) : 51-67.
PMID 15821778
 
Interleukin 1alpha and tissue-lytic matrix metalloproteinase-1 are elevated in ectopic endometrium of patients with endometriosis.
Hudelist G, Lass H, Keckstein J, Walter I, Wieser F, Wenzl R, Mueller R, Czerwenka K, Kubista E, Singer CF
Human reproduction (Oxford, England). 2005 ; 20 (6) : 1695-1701.
PMID 15746198
 
Differential frequencies of p16(INK4a) promoter hypermethylation, p53 mutation, and K-ras mutation in exfoliative material mark the development of lung cancer in symptomatic chronic smokers.
Kersting M, Friedl C, Kraus A, Behn M, Pankow W, Schuermann M
Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2000 ; 18 (18) : 3221-3229.
PMID 10986054
 
p16(INK4a) and histology-specific methylation of CpG islands by exposure to tobacco smoke in non-small cell lung cancer.
Kim DH, Nelson HH, Wiencke JK, Zheng S, Christiani DC, Wain JC, Mark EJ, Kelsey KT
Cancer research. 2001 ; 61 (8) : 3419-3424.
PMID 11309302
 
S100A13, a new marker of angiogenesis in human astrocytic gliomas.
Landriscina M, Schinzari G, Di Leonardo G, Quirino M, Cassano A, D'Argento E, Lauriola L, Scerrati M, Prudovsky I, Barone C
Journal of neuro-oncology. 2006 ; 80 (3) : 251-259.
PMID 16773219
 
Crystal structure study on human S100A13 at 2.0 A resolution.
Li M, Zhang PF, Pan XW, Chang WR
Biochemical and biophysical research communications. 2007 ; 356 (3) : 616-621.
PMID 17374362
 
S100A13 mediates the copper-dependent stress-induced release of IL-1alpha from both human U937 and murine NIH 3T3 cells.
Mandinova A, Soldi R, Graziani I, Bagala C, Bellum S, Landriscina M, Tarantini F, Prudovsky I, Maciag T
Journal of cell science. 2003 ; 116 (Pt 13) : 2687-2696.
PMID 12746488
 
Identification of a novel, functional role for S100A13 in invasive lung cancer cell lines.
Pierce A, Barron N, Linehan R, Ryan E, O'Driscoll L, Daly C, Clynes M
European journal of cancer (Oxford, England : 1990). 2008 ; 44 (1) : 151-159.
PMID 18061437
 
The non-classical export routes: FGF1 and IL-1alpha point the way.
Prudovsky I, Mandinova A, Soldi R, Bagala C, Graziani I, Landriscina M, Tarantini F, Duarte M, Bellum S, Doherty H, Maciag T
Journal of cell science. 2003 ; 116 (Pt 24) : 4871-4881.
PMID 14625381
 
S100A13. Biochemical characterization and subcellular localization in different cell lines.
Ridinger K, Schäfer BW, Durussel I, Cox JA, Heizmann CW
The Journal of biological chemistry. 2000 ; 275 (12) : 8686-8694.
PMID 10722710
 
Bacterial infection and semen quality.
Sanocka-Maciejewska D, Ciupiń M, Kurpisz M
Journal of reproductive immunology. 2005 ; 67 (1-2) : 51-56.
PMID 16112738
 
Three distinct anti-allergic drugs, amlexanox, cromolyn and tranilast, bind to S100A12 and S100A13 of the S100 protein family.
Shishibori T, Oyama Y, Matsushita O, Yamashita K, Furuichi H, Okabe A, Maeta H, Hata Y, Kobayashi R
The Biochemical journal. 1999 ; 338 ( Pt 3) : 583-589.
PMID 10051426
 
Characterization of the human and mouse cDNAs coding for S100A13, a new member of the S100 protein family.
Wicki R, Schäfer BW, Erne P, Heizmann CW
Biochemical and biophysical research communications. 1996 ; 227 (2) : 594-599.
PMID 8878558
 
Molecular genetics of small cell lung carcinoma.
Wistuba II, Gazdar AF, Minna JD
Seminars in oncology. 2001 ; 28 (2 Suppl 4) : 3-13.
PMID 11479891
 

Citation

This paper should be referenced as such :
Barone, C ; Bagal, C ; Landriscina, M
S100A13 (S100 calcium binding protein A13)
Atlas Genet Cytogenet Oncol Haematol. 2008;12(6):440-442.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/S100A13ID44197ch1q21.html


External links

Nomenclature
HGNC (Hugo)S100A13   10490
Cards
AtlasS100A13ID44197ch1q21
Entrez_Gene (NCBI)S100A13  6284  S100 calcium binding protein A13
Aliases
GeneCards (Weizmann)S100A13
Ensembl hg19 (Hinxton)ENSG00000189171 [Gene_View]  chr1:153591276-153606568 [Contig_View]  S100A13 [Vega]
Ensembl hg38 (Hinxton)ENSG00000189171 [Gene_View]  chr1:153591276-153606568 [Contig_View]  S100A13 [Vega]
ICGC DataPortalENSG00000189171
TCGA cBioPortalS100A13
AceView (NCBI)S100A13
Genatlas (Paris)S100A13
WikiGenes6284
SOURCE (Princeton)S100A13
Genetics Home Reference (NIH)S100A13
Genomic and cartography
GoldenPath hg19 (UCSC)S100A13  -     chr1:153591276-153606568 -  1q21   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)S100A13  -     1q21   [Description]    (hg38-Dec_2013)
EnsemblS100A13 - 1q21 [CytoView hg19]  S100A13 - 1q21 [CytoView hg38]
Mapping of homologs : NCBIS100A13 [Mapview hg19]  S100A13 [Mapview hg38]
OMIM601989   
Gene and transcription
Genbank (Entrez)AA366085 AK097132 AY987392 BC000632 BC068064
RefSeq transcript (Entrez)NM_001024210 NM_001024211 NM_001024212 NM_001024213 NM_005979
RefSeq genomic (Entrez)NC_000001 NC_018912 NT_004487 NW_004929293
Consensus coding sequences : CCDS (NCBI)S100A13
Cluster EST : UnigeneHs.516505 [ NCBI ]
CGAP (NCI)Hs.516505
Alternative Splicing GalleryENSG00000189171
Gene ExpressionS100A13 [ NCBI-GEO ]   S100A13 [ EBI - ARRAY_EXPRESS ]   S100A13 [ SEEK ]   S100A13 [ MEM ]
Gene Expression Viewer (FireBrowse)S100A13 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6284
GTEX Portal (Tissue expression)S100A13
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99584   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ99584  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ99584
Splice isoforms : SwissVarQ99584
PhosPhoSitePlusQ99584
Domains : Interpro (EBI)EF-hand-dom_pair    S100_Ca-bd_sub    S100A13   
Domain families : Pfam (Sanger)S_100 (PF01023)   
Domain families : Pfam (NCBI)pfam01023   
Conserved Domain (NCBI)S100A13
DMDM Disease mutations6284
Blocks (Seattle)S100A13
PDB (SRS)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
PDB (PDBSum)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
PDB (IMB)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
PDB (RSDB)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
Structural Biology KnowledgeBase1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
SCOP (Structural Classification of Proteins)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
CATH (Classification of proteins structures)1YUR    1YUS    1YUT    1YUU    2EGD    2H2K    2K8M    2KI4    2KI6    2KOT    2L5X    2LE9   
SuperfamilyQ99584
Human Protein AtlasENSG00000189171
Peptide AtlasQ99584
HPRD03586
IPIIPI00016179   
Protein Interaction databases
DIP (DOE-UCLA)Q99584
IntAct (EBI)Q99584
FunCoupENSG00000189171
BioGRIDS100A13
STRING (EMBL)S100A13
ZODIACS100A13
Ontologies - Pathways
QuickGOQ99584
Ontology : AmiGOcopper ion binding  calcium ion binding  protein binding  extracellular space  nucleus  cytoplasm  cytosol  zinc ion binding  positive regulation of cell proliferation  lipid binding  regulation of cell shape  fibroblast growth factor binding  mast cell granule  protein homodimerization activity  positive regulation of I-kappaB kinase/NF-kappaB signaling  mast cell degranulation  response to copper ion  perinuclear region of cytoplasm  cytokine secretion  interleukin-1 alpha secretion  RAGE receptor binding  response to electrical stimulus  extracellular exosome  
Ontology : EGO-EBIcopper ion binding  calcium ion binding  protein binding  extracellular space  nucleus  cytoplasm  cytosol  zinc ion binding  positive regulation of cell proliferation  lipid binding  regulation of cell shape  fibroblast growth factor binding  mast cell granule  protein homodimerization activity  positive regulation of I-kappaB kinase/NF-kappaB signaling  mast cell degranulation  response to copper ion  perinuclear region of cytoplasm  cytokine secretion  interleukin-1 alpha secretion  RAGE receptor binding  response to electrical stimulus  extracellular exosome  
NDEx NetworkS100A13
Atlas of Cancer Signalling NetworkS100A13
Wikipedia pathwaysS100A13
Orthology - Evolution
OrthoDB6284
GeneTree (enSembl)ENSG00000189171
Phylogenetic Trees/Animal Genes : TreeFamS100A13
HOVERGENQ99584
HOGENOMQ99584
Homologs : HomoloGeneS100A13
Homology/Alignments : Family Browser (UCSC)S100A13
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerS100A13 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)S100A13
dbVarS100A13
ClinVarS100A13
1000_GenomesS100A13 
Exome Variant ServerS100A13
ExAC (Exome Aggregation Consortium)S100A13 (select the gene name)
Genetic variants : HAPMAP6284
Genomic Variants (DGV)S100A13 [DGVbeta]
DECIPHER (Syndromes)1:153591276-153606568  ENSG00000189171
CONAN: Copy Number AnalysisS100A13 
Mutations
ICGC Data PortalS100A13 
TCGA Data PortalS100A13 
Broad Tumor PortalS100A13
OASIS PortalS100A13 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICS100A13  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDS100A13
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 S100A13
DgiDB (Drug Gene Interaction Database)S100A13
DoCM (Curated mutations)S100A13 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)S100A13 (select a term)
intoGenS100A13
NCG5 (London)S100A13
Cancer3DS100A13(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601989   
Orphanet
MedgenS100A13
Genetic Testing Registry S100A13
NextProtQ99584 [Medical]
TSGene6284
GENETestsS100A13
Huge Navigator S100A13 [HugePedia]
snp3D : Map Gene to Disease6284
BioCentury BCIQS100A13
ClinGenS100A13
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6284
Chemical/Pharm GKB GenePA34902
Clinical trialS100A13
Miscellaneous
canSAR (ICR)S100A13 (select the gene name)
Probes
Litterature
PubMed38 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineS100A13
EVEXS100A13
GoPubMedS100A13
iHOPS100A13
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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