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mutLBSgeneDB |
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| Gene summary for SDS |
 Gene summary |
| Basic gene Info. | Gene symbol | SDS |
| Gene name | serine dehydratase | |
| Synonyms | SDH | |
| Cytomap | UCSC genome browser: 12q24.13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_006843.2, | |
| Description | L-serine ammonia-lyaseL-serine deaminaseL-serine dehydrataseL-serine dehydratase/L-threonine deaminaseL-threonine dehydrataseTDH | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 182128 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000135094 | ||
| HPRD : 01633 | ||
| Vega : OTTHUMG00000169554 | ||
| Protein | UniProt: P20132 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SDS | |
| BioGPS: 10993 | ||
| Pathway | NCI Pathway Interaction Database: SDS | |
| KEGG: SDS | ||
| REACTOME: SDS | ||
| Pathway Commons: SDS | ||
| Context | iHOP: SDS | |
| ligand binding site mutation search in PubMed: SDS | ||
| UCL Cancer Institute: SDS | ||
| 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:0006565 | L-serine catabolic process | 15689518 | GO:0042866 | pyruvate biosynthetic process | 15689518 |
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| Ligand binding site mutations for SDS |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G170 | G170W | 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 SDS |
| 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 |
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| 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 | G170 | G170W | 0.74489049 |
| (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 SDS from PDB |
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| Differential gene expression and gene-gene network for SDS |
| 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 SDS |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for SDS |
| 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Nutraceutical | DB00114 | Pyridoxal Phosphate | Small molecule |  |
| Approved|nutraceutical | DB00133 | L-Serine | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of SDS go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | PLP | PYRIDOXAL 5'-PHOSPHATE | 1p5j | A | G170 |
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| Conservation information for LBS of SDS |
| Multiple alignments for P20132 in multiple species |
| LBS | AA sequence | # species | Species | A222 | TSVAKALGVNT | 2 | Mus musculus, Rattus norvegicus | A222 | TSVAKALGVKT | 1 | Homo sapiens | A222 | TSVAKALGVTT | 1 | Bos taurus | A269 | ILVEPACGAAL | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | C303 | LVVIVCGGSNI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F40 | QPSGSFKIRGI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G168 | IVLSVGGGGLL | 2 | Mus musculus, Rattus norvegicus | G168 | IALSVGGGGLL | 1 | Homo sapiens | G168 | IVLAVGGGGLL | 1 | Bos taurus | G169 | VLSVGGGGLLC | 2 | Mus musculus, Rattus norvegicus | G169 | ALSVGGGGLLC | 1 | Homo sapiens | G169 | VLAVGGGGLLC | 1 | Bos taurus | G170 | LSVGGGGLLCG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G170 | LAVGGGGLLCG | 1 | Bos taurus | G171 | SVGGGGLLCGV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G171 | AVGGGGLLCGV | 1 | Bos taurus | G304 | VVIVCGGSNIS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G305 | VIVCGGSNISL | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K41 | PSGSFKIRGIG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L172 | VGGGGLLCGVV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L223 | SVAKALGVNTV | 2 | Mus musculus, Rattus norvegicus | L223 | SVAKALGVKTV | 1 | Homo sapiens | L223 | SVAKALGVTTV | 1 | Bos taurus | N67 | ---AGNAGMAA | 2 | Homo sapiens, Bos taurus | N67 | ---AGNAGMAT | 1 | Mus musculus | N67 | PLTAGNAGMAT | 1 | Rattus norvegicus | S166 | GAIVLSVGGGG | 2 | Mus musculus, Rattus norvegicus | S166 | GAIALSVGGGG | 1 | Homo sapiens | S166 | GAIVLAVGGGG | 1 | Bos taurus | V167 | AIVLSVGGGGL | 2 | Mus musculus, Rattus norvegicus | V167 | AIALSVGGGGL | 1 | Homo sapiens | V167 | AIVLAVGGGGL | 1 | Bos taurus |
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