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SS18L1 (synovial sarcoma translocation gene on chromosome 18-like 1)

Written2005-03Clelia Tiziana Storlazzi, Fredrik Mertens, Ioannis Panagopoulos
Department of Clinical Genetics, Lund University Hospital, Lund, Sweden (FM, IP)

(Note : for Links provided by Atlas : click)

Identity

Alias_namessynovial sarcoma translocation gene on chromosome 18-like 1
Alias_symbol (synonym)KIAA0693
CREST
Other aliasMGC26711
SYT homolog 1
HGNC (Hugo) SS18L1
LocusID (NCBI) 26039
Atlas_Id 474
Location 20q13.33  [Link to chromosome band 20q13]
Location_base_pair Starts at 62143720 and ends at 62182510 bp from pter ( according to hg19-Feb_2009)  [Mapping SS18L1.png]
Local_order chr20:60,152,245-60,190,935 (UCSC latest release: May 2004)
Fusion genes
(updated 2016)
SS18L1 (20q13.33) / CDH4 (20q13.33)SS18L1 (20q13.33) / SSX1 (Xp11.23)SS18L1 (20q13.33) / SSX2 (Xp11.22)
SS18L1 (20q13.33) / SSX4 (Xp11.23)SS18L1 (20q13.33) / TAF4 (20q13.33)SSX1 (Xp11.23) / SS18L1 (20q13.33)
SSX2 (Xp11.22) / SS18L1 (20q13.33)SSX4 (Xp11.23) / SS18L1 (20q13.33)

DNA/RNA

Note Member of the SS18 family.
Description 11 exons with similar splice sites as SS18.The promoter region lacks CAAT and TATA boxes but contains CpG islands, suggesting that SS18L1 is a housekeeping gene.
Pseudogene SS18L2 (3p21)

Protein

Description 396 amino acids, 42990 Da. The SS18L1 protein, similarly to the SS18 protein, exhibits two domains: a SYT N-terminal homology domain found in a wide variety of species ranging from plants to humans and the QPGY domain at the COOH-terminal part, rich in glutamine, proline, glycine, and tyrosine. The QPGY domain of the SS18 protein may activate transcription when coupled to a DNA-binding domain.
Expression Ubiquitous; with lowest levels in spleen.
Localisation Nuclear?
Function Calcium-responsive transactivator: CREST is a SYT -related nuclear protein that interacts with CREB-binding protein (CBP) and is expressed in the developing brain.
Homology SS18, SS18L2

Implicated in

Note
Disease Synovial sarcoma
Prognosis Unknown
Cytogenetics t(X;20)(p11;q13.3)
Hybrid/Mutated Gene In the SS18L1/ SSX1 transcript detected in the synovial sarcoma, the exon 10 of SS18L1, which corresponds to exon 10 of SS18, was fused to exon 6 of SSX1
Abnormal Protein In the putative SS18L1/SSX1 chimeric protein, the last 8 amino acid residues of the SS18L1 protein are replaced by 78 amino acids from the COOH-terminal part of SSX1. By analogy with what is presumed to be the case for the SS18/SSX fusion protein, SS18L1/SSX1 is likely to show an altered transcriptional pattern with the COOH-terminal SSX domain, redirecting the SS18L1 activation domain to new target promoters.
  

Bibliography

Dendrite development regulated by CREST, a calcium-regulated transcriptional activator.
Aizawa H, Hu SC, Bobb K, Balakrishnan K, Ince G, Gurevich I, Cowan M, Ghosh A
Science (New York, N.Y.). 2004 ; 303 (5655) : 197-202.
PMID 14716005
 
Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro.
Ishikawa K, Nagase T, Suyama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O
DNA research : an international journal for rapid publication of reports on genes and genomes. 1998 ; 5 (3) : 169-176.
PMID 9734811
 
A novel fusion gene, SS18L1/SSX1, in synovial sarcoma.
Storlazzi CT, Mertens F, Mandahl N, Gisselsson D, Isaksson M, Gustafson P, Domanski HA, Panagopoulos I
Genes, chromosomes & cancer. 2003 ; 37 (2) : 195-200.
PMID 12696068
 
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Mammalian Gene Collection Program Team, Marra MA
Proceedings of the National Academy of Sciences of the United States of America. 2002 ; 99 (26) : 16899-16903.
PMID 12477932
 
Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene.
de Bruijn DR, Kater-Baats E, Eleveld M, Merkx G, Geurts Van Kessel A
Cytogenetics and cell genetics. 2001 ; 92 (3-4) : 310-319.
PMID 11435705
 

Citation

This paper should be referenced as such :
Storlazzi, CT ; Mertens, F ; Panagopoulos, I
SS18L1 (synovial sarcoma translocation gene on chromosome 18-like 1)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(2):141-142.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SS18L1ID474ch20q13.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Soft Tissues: Biphasic svial sarcoma with t(X;20)(p11;q13) SS18L1/SSX1


External links

Nomenclature
HGNC (Hugo)SS18L1   15592
Cards
AtlasSS18L1ID474ch20q13
Entrez_Gene (NCBI)SS18L1  26039  SS18L1, nBAF chromatin remodeling complex subunit
AliasesCREST; LP2261
GeneCards (Weizmann)SS18L1
Ensembl hg19 (Hinxton)ENSG00000184402 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000184402 [Gene_View]  chr20:62143720-62182510 [Contig_View]  SS18L1 [Vega]
ICGC DataPortalENSG00000184402
TCGA cBioPortalSS18L1
AceView (NCBI)SS18L1
Genatlas (Paris)SS18L1
WikiGenes26039
SOURCE (Princeton)SS18L1
Genetics Home Reference (NIH)SS18L1
Genomic and cartography
GoldenPath hg38 (UCSC)SS18L1  -     chr20:62143720-62182510 +  20q13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SS18L1  -     20q13.33   [Description]    (hg19-Feb_2009)
EnsemblSS18L1 - 20q13.33 [CytoView hg19]  SS18L1 - 20q13.33 [CytoView hg38]
Mapping of homologs : NCBISS18L1 [Mapview hg19]  SS18L1 [Mapview hg38]
OMIM606472   
Gene and transcription
Genbank (Entrez)AB014593 AK125656 AK291485 AK299881 AK308765
RefSeq transcript (Entrez)NM_001301778 NM_015558 NM_198935
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SS18L1
Cluster EST : UnigeneHs.154429 [ NCBI ]
CGAP (NCI)Hs.154429
Alternative Splicing GalleryENSG00000184402
Gene ExpressionSS18L1 [ NCBI-GEO ]   SS18L1 [ EBI - ARRAY_EXPRESS ]   SS18L1 [ SEEK ]   SS18L1 [ MEM ]
Gene Expression Viewer (FireBrowse)SS18L1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)26039
GTEX Portal (Tissue expression)SS18L1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75177   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75177  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75177
Splice isoforms : SwissVarO75177
PhosPhoSitePlusO75177
Domains : Interpro (EBI)SS18_fam   
Domain families : Pfam (Sanger)SSXT (PF05030)   
Domain families : Pfam (NCBI)pfam05030   
Conserved Domain (NCBI)SS18L1
DMDM Disease mutations26039
Blocks (Seattle)SS18L1
SuperfamilyO75177
Human Protein AtlasENSG00000184402
Peptide AtlasO75177
HPRD09398
IPIIPI00954989   IPI00954973   IPI00955028   IPI00028722   IPI00747811   
Protein Interaction databases
DIP (DOE-UCLA)O75177
IntAct (EBI)O75177
FunCoupENSG00000184402
BioGRIDSS18L1
STRING (EMBL)SS18L1
ZODIACSS18L1
Ontologies - Pathways
QuickGOO75177
Ontology : AmiGOkinetochore  condensed chromosome kinetochore  condensed nuclear chromosome, centromeric region  transcription coactivator activity  protein binding  nucleus  nucleus  cytosol  transcription, DNA-templated  dendrite development  covalent chromatin modification  nuclear body  positive regulation of transcription, DNA-templated  positive regulation of dendrite morphogenesis  nBAF complex  
Ontology : EGO-EBIkinetochore  condensed chromosome kinetochore  condensed nuclear chromosome, centromeric region  transcription coactivator activity  protein binding  nucleus  nucleus  cytosol  transcription, DNA-templated  dendrite development  covalent chromatin modification  nuclear body  positive regulation of transcription, DNA-templated  positive regulation of dendrite morphogenesis  nBAF complex  
NDEx NetworkSS18L1
Atlas of Cancer Signalling NetworkSS18L1
Wikipedia pathwaysSS18L1
Orthology - Evolution
OrthoDB26039
GeneTree (enSembl)ENSG00000184402
Phylogenetic Trees/Animal Genes : TreeFamSS18L1
HOVERGENO75177
HOGENOMO75177
Homologs : HomoloGeneSS18L1
Homology/Alignments : Family Browser (UCSC)SS18L1
Gene fusions - Rearrangements
Fusion : MitelmanSS18L1/CDH4 [20q13.33/20q13.33]  
Fusion : MitelmanSS18L1/SSX1 [20q13.33/Xp11.23]  [t(X;20)(p11;q13)]  
Fusion : COSMICSS18L1 [20q13.33]  -  SSX1 [Xp11.23]  [fusion_1123]  [fusion_1124]  
Fusion: TCGASS18L1 20q13.33 CDH4 20q13.33 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSS18L1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SS18L1
dbVarSS18L1
ClinVarSS18L1
1000_GenomesSS18L1 
Exome Variant ServerSS18L1
ExAC (Exome Aggregation Consortium)SS18L1 (select the gene name)
Genetic variants : HAPMAP26039
Genomic Variants (DGV)SS18L1 [DGVbeta]
DECIPHERSS18L1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSS18L1 
Mutations
ICGC Data PortalSS18L1 
TCGA Data PortalSS18L1 
Broad Tumor PortalSS18L1
OASIS PortalSS18L1 [ Somatic mutations - Copy number]
Cancer Gene: CensusSS18L1 
Somatic Mutations in Cancer : COSMICSS18L1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSS18L1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SS18L1
DgiDB (Drug Gene Interaction Database)SS18L1
DoCM (Curated mutations)SS18L1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SS18L1 (select a term)
intoGenSS18L1
NCG5 (London)SS18L1
Cancer3DSS18L1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606472   
Orphanet
MedgenSS18L1
Genetic Testing Registry SS18L1
NextProtO75177 [Medical]
TSGene26039
GENETestsSS18L1
Target ValidationSS18L1
Huge Navigator SS18L1 [HugePedia]
snp3D : Map Gene to Disease26039
BioCentury BCIQSS18L1
ClinGenSS18L1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD26039
Chemical/Pharm GKB GenePA37989
Clinical trialSS18L1
Miscellaneous
canSAR (ICR)SS18L1 (select the gene name)
Probes
Litterature
PubMed29 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSS18L1
EVEXSS18L1
GoPubMedSS18L1
iHOPSS18L1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 18 17:15:22 CEST 2017

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