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mutLBSgeneDB |
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| Gene summary for SETD2 |
 Gene summary |
| Basic gene Info. | Gene symbol | SETD2 |
| Gene name | SET domain containing 2 | |
| Synonyms | HBP231|HIF-1|HIP-1|HYPB|KMT3A|SET2|p231HBP | |
| Cytomap | UCSC genome browser: 3p21.31 | |
| Type of gene | protein-coding | |
| RefGenes | NM_014159.6, NM_012271.1, | |
| Description | histone-lysine N-methyltransferase SETD2huntingtin interacting protein 1huntingtin yeast partner Bhuntingtin-interacting protein Blysine N-methyltransferase 3A | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 612778 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000181555 | ||
| HPRD : 11043 | ||
| Vega : OTTHUMG00000133514 | ||
| Protein | UniProt: Q9BYW2 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SETD2 | |
| BioGPS: 29072 | ||
| Pathway | NCI Pathway Interaction Database: SETD2 | |
| KEGG: SETD2 | ||
| REACTOME: SETD2 | ||
| Pathway Commons: SETD2 | ||
| Context | iHOP: SETD2 | |
| ligand binding site mutation search in PubMed: SETD2 | ||
| UCL Cancer Institute: SETD2 | ||
| 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:0097198 | histone H3-K36 trimethylation | 23043551 |
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| Ligand binding site mutations for SETD2 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | C1501 | C1501Y | COAD | 2 | H1629 | H1629Y | BLCA | 1 | Y1666,R1670 | F1668L | BRCA | 1 | R1625 | R1625L | BRCA | 1 | C1501 | C1501R | BRCA | 1 | H1629 | C1631Y | COAD | 1 | H1629 | C1631R | COAD | 1 | C1501 | C1501R | COAD | 1 | H1603 | H1603R | HNSC | 1 | C1499 | C1499Y | KIRC | 1 | R1625 | R1625H | KIRC | 1 | M1627 | M1627R | KIRC | 1 | Y1666 | Y1666H | KIRC | 1 | Y1666,F1664 | D1665V | KIRC | 1 | H1629 | H1629Y | KIRC | 1 | R1625 | R1625C | KIRC | 1 | K1560 | K1560N | LUAD | 1 | C1516 | C1516F | LUAD | 1 | R1625 | S1624C | LUAD | 1 | C1516 | G1517V | LUAD | 1 | C1501 | C1501S | LUAD | 1 | R1625 | R1625H | LUSC | 1 | H1629 | H1629Y | SKCM | 1 | K1560 | K1560R | UCEC | 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. |
| Clinical information for SETD2 from My Cancer Genome. |
| SET domain containing 2 (SETD2) is a gene that encodes a protein that is a member of a class of huntingtin interacting proteins. The protein functions as a histone methyltransferase specific for lysine-36 of histone H3. Missense mutations, nonsense mutations, silent mutations, frameshift deletions and insertions, and in-frame deletions are observed in cancers such as endometrial cancer, intestinal cancer, and kidney cancer.Related Pathways:Chromatin remodeling/DNA methylation.Modified: December 4, 2015 |
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| Protein structure related information for SETD2 |
| 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 | C1516 | G1517V | 0.22832397 | M1627 | M1627R | -1.0582841 | C1501 | C1501S | -1.0260146 | Y1666 | Y1666H | -1.0127526 | H1603 | H1603R | -1.0121387 | R1625 | R1625H | -0.9708563 | F1664 | D1665V | -0.95837224 | Y1666 | D1665V | -0.95837224 | C1516 | C1516F | -0.80189487 | C1499 | C1499Y | -0.80017829 | C1501 | C1501R | -0.74527506 | R1625 | R1625C | -0.73185813 | C1501 | C1501Y | -0.7178922 | R1625 | S1624C | -0.69183267 | K1560 | K1560N | -0.66067542 | H1629 | H1629Y | -0.54816527 | H1629 | C1631R | -0.54408433 | H1629 | C1631Y | -0.48045278 | R1625 | R1625L | -0.40779417 | K1560 | K1560R | -0.30392532 | Y1666 | F1668L | -0.30255286 | R1670 | F1668L | -0.30255286 |
| (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 SETD2 from PDB |
| PDB ID | PDB title | PDB structure | 2A7O | Solution Structure of the hSet2/HYPB SRI domain |  |
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| Differential gene expression and gene-gene network for SETD2 |
| 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 SETD2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0007134 | Carcinoma, Renal Cell | 14 | Biomarker |
| umls:C0023418 | Leukemia | 4 | Biomarker |
| umls:C0010606 | Carcinoma, Adenoid Cystic | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for SETD2 |
| 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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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of SETD2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 4fmu | A | C1499 C1501 C1516 | ZN | ZINC(2+) | 4h12 | A | C1499 C1501 C1516 | ZN | ZINC(2+) | 4fmu | A | C1516 | ZN | ZINC(2+) | 4h12 | A | C1516 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 4h12 | A | K1560 H1603 R1625 H1629 Y1666 R1670 | 0UM | (2S,5S)-2-AMINO-6-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9- YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-5- (PROPYLAMINO)HEXANOIC ACID | 4fmu | A | K1560 H1603 R1625 M1627 H1629 F1664 Y1666 |
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| Conservation information for LBS of SETD2 |
| Multiple alignments for Q9BYW2 in multiple species |
| LBS | AA sequence | # species | Species |
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