mutLBSgeneDB |
Gene summary for SDCBP |
Gene summary |
Basic gene Info. | Gene symbol | SDCBP |
Gene name | syndecan binding protein (syntenin) | |
Synonyms | MDA-9|MDA9|ST1|SYCL|TACIP18 | |
Cytomap | UCSC genome browser: 8q12 | |
Type of gene | protein-coding | |
RefGenes | NM_001007067.1, NM_001007068.1,NM_001007069.1,NM_001007070.1,NM_005625.3, | |
Description | melanoma differentiation associated protein-9melanoma differentiation-associated protein 9pro-TGF-alpha cytoplasmic domain-interacting protein 18scaffold protein Pbp1syndecan-binding protein 1syntenin-1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 602217 | |
HGNC : HGNC | ||
Ensembl : ENSG00000137575 | ||
HPRD : 03741 | ||
Vega : OTTHUMG00000164303 | ||
Protein | UniProt: O00560 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SDCBP | |
BioGPS: 6386 | ||
Pathway | NCI Pathway Interaction Database: SDCBP | |
KEGG: SDCBP | ||
REACTOME: SDCBP | ||
Pathway Commons: SDCBP | ||
Context | iHOP: SDCBP | |
ligand binding site mutation search in PubMed: SDCBP | ||
UCL Cancer Institute: SDCBP | ||
Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0042327 | positive regulation of phosphorylation | 18256285 |
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Ligand binding site mutations for SDCBP |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | V209 | V209I | HNSC | 1 | A255 | A255V | STAD | 1 |
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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Protein structure related information for SDCBP |
Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
: nsSNV at non-LBS: nsSNV at LBS |
nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
LBS | AAchange of nsSNV | Relative stability change | A255 | A255V | -0.45742732 | V209 | V209I | -0.44957309 |
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
Structure image for SDCBP from PDB |
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Differential gene expression and gene-gene network for SDCBP |
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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Phenotype information for SDCBP |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0029408 | Osteoarthritis | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for SDCBP |
Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of SDCBP go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ASN,GLU,TYR,LYS,VAL) | 1v1t | B | V209 | III | Peptide ligand (GLU,PHE,TYR,ALA) | 1ybo | B | V209 | III | Peptide ligand (ASP,SER,VAL,PHE) | 1obx | A | V209 A255 | III | Peptide ligand (ASN,GLU,PHE,TYR,ALA) | 1oby | A | V209 A255 | III | Peptide ligand (THR,ASN,GLU,PHE,TYR,ALA) | 1oby | B | V209 A255 | III | Peptide ligand (ASP,SER,VAL,PHE) | 1obz | A | V209 A255 | III | Peptide ligand (ASN,GLU,TYR,LYS,VAL) | 1v1t | A | V209 A255 | III | Peptide ligand (ASN,GLU,PHE,TYR,PHE) | 1w9e | A | V209 A255 | III | Peptide ligand (ASN,GLU,PHE,TYR,PHE) | 1w9e | B | V209 A255 | III | Peptide ligand (ASN,GLU,TYR,TYR,VAL) | 1w9o | A | V209 A255 | III | Peptide ligand (ASN,GLU,TYR,TYR,VAL) | 1w9o | B | V209 A255 | III | Peptide ligand (ASN,GLU,PHE,ALA,PHE) | 1w9q | B | V209 A255 | III | Peptide ligand (THR,ASN,GLU,PHE,TYR,ALA) | 1ybo | A | V209 A255 |
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Conservation information for LBS of SDCBP |
Multiple alignments for O00560 in multiple species |
LBS | AA sequence | # species | Species | A255 | KDAQIADILST | 2 | Mus musculus, Rattus norvegicus | A255 | KDSQIADILST | 1 | Homo sapiens | C239 | TDHHICEINGQ | 2 | Mus musculus, Rattus norvegicus | C239 | TEHNICEINGQ | 1 | Homo sapiens | D251 | VIGLKDAQIAD | 2 | Mus musculus, Rattus norvegicus | D251 | VIGLKDSQIAD | 1 | Homo sapiens | E240 | DHHICEINGQN | 2 | Mus musculus, Rattus norvegicus | E240 | EHNICEINGQN | 1 | Homo sapiens | F211 | SGHVGFIFKSG | 2 | Mus musculus, Rattus norvegicus | F211 | TGHVGFIFKNG | 1 | Homo sapiens | F213 | HVGFIFKSGKI | 2 | Mus musculus, Rattus norvegicus | F213 | HVGFIFKNGKI | 1 | Homo sapiens | G126 | QDGKIGLRLKS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G210 | SSGHVGFIFKS | 2 | Mus musculus, Rattus norvegicus | G210 | STGHVGFIFKN | 1 | Homo sapiens | H175 | SSDKAHKVLKQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H208 | KDSSGHVGFIF | 2 | Mus musculus, Rattus norvegicus | H208 | KDSTGHVGFIF | 1 | Homo sapiens | I125 | DQDGKIGLRLK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I212 | GHVGFIFKSGK | 2 | Mus musculus, Rattus norvegicus | I212 | GHVGFIFKNGK | 1 | Homo sapiens | I254 | LKDAQIADILS | 2 | Mus musculus, Rattus norvegicus | I254 | LKDSQIADILS | 1 | Homo sapiens | K124 | KDQDGKIGLRL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K214 | VGFIFKSGKIT | 2 | Mus musculus, Rattus norvegicus | K214 | VGFIFKNGKIT | 1 | Homo sapiens | L127 | DGKIGLRLKSI | 2 | Homo sapiens, Mus musculus | L127 | DGKIGLRLKSV | 1 | Rattus norvegicus | L258 | QIADILSTAGT | 2 | Mus musculus, Rattus norvegicus | L258 | QIADILSTSGT | 1 | Homo sapiens | N245 | EINGQNVIGLK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q142 | FVQLVQANSPA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R128 | GKIGLRLKSID | 2 | Homo sapiens, Mus musculus | R128 | GKIGLRLKSVD | 1 | Rattus norvegicus | S252 | IGLKDAQIADI | 2 | Mus musculus, Rattus norvegicus | S252 | IGLKDSQIADI | 1 | Homo sapiens | V209 | DSSGHVGFIFK | 2 | Mus musculus, Rattus norvegicus | V209 | DSTGHVGFIFK | 1 | Homo sapiens | V222 | KITSIVKDSSA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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