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mutLBSgeneDB |
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| Gene summary for TCN2 |
 Gene summary |
| Basic gene Info. | Gene symbol | TCN2 |
| Gene name | transcobalamin II | |
| Synonyms | D22S676|D22S750|II|TC|TC II|TC-2|TC2|TCII | |
| Cytomap | UCSC genome browser: 22q12.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000355.3, NM_001184726.1,NM_001190420.1, | |
| Description | macrocytic anemiatranscobalamin II; macrocytic anemiatranscobalamin-2vitamin B12-binding protein 2 | |
| Modification date | 20141221 | |
| dbXrefs | MIM : 613441 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000185339 | ||
| HPRD : 02037 | ||
| Vega : OTTHUMG00000151095 | ||
| Protein | UniProt: P20062 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TCN2 | |
| BioGPS: 6948 | ||
| Pathway | NCI Pathway Interaction Database: TCN2 | |
| KEGG: TCN2 | ||
| REACTOME: TCN2 | ||
| Pathway Commons: TCN2 | ||
| Context | iHOP: TCN2 | |
| ligand binding site mutation search in PubMed: TCN2 | ||
| UCL Cancer Institute: TCN2 | ||
| 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 |
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| Ligand binding site mutations for TCN2 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | W41 | W41L | COAD | 1 | L397 | L398I | COAD | 1 | H191 | S192F | HNSC | 1 | W41 | M42T | OV | 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 TCN2 |
| 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 | W41 | M42T | -1.319633 | W41 | W41L | -0.98494542 | H191 | S192F | -0.44602378 | L397 | L398I | -0.33855004 |
| (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 TCN2 from PDB |
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| Differential gene expression and gene-gene network for TCN2 |
| 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 TCN2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0002888 | Anemia, Megaloblastic | 4 | Biomarker |
| umls:C0008924 | Cleft Lip | 3 | Biomarker, GeneticVariation |
| umls:C0001430 | Adenoma | 1 | Biomarker |
| umls:C0004352 | Autistic Disorder | 1 | Biomarker |
| umls:C0009404 | Colorectal Neoplasms | 1 | Biomarker |
| umls:C3658338 | Drug-Related Side Effects and Adverse Reactions | 1 | Biomarker |
| umls:C0270612 | Leukoencephalopathies | 1 | Biomarker |
| umls:C0033578 | Prostatic Neoplasms | 1 | Biomarker |
| umls:C0342701 | Transcobalamin II deficiency | 1 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TCN2 |
| 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 TCN2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of TCN2 |
| Multiple alignments for P20062 in multiple species |
| LBS | AA sequence | # species | Species | D194 | GHHSVDTAAMA | 1 | Homo sapiens | D194 | DHVSVDTMAMA | 1 | Bos taurus | D194 | GHVSVDTEAMA | 1 | Mus musculus | F394 | AGEREFWQLLR | 1 | Homo sapiens | F394 | AGEREFWQVLR | 1 | Bos taurus | F394 | AGDREYWQLLR | 1 | Mus musculus | G103 | GKPSMGQLALY | 1 | Homo sapiens | G103 | AKPSMGQLALY | 1 | Bos taurus | G103 | PKLSGGSLALY | 1 | Mus musculus | G378 | QASLSGPYLTS | 2 | Homo sapiens, Mus musculus | G378 | QASLSGPFLTS | 1 | Bos taurus | G408 | TPLLQGIADYR | 1 | Homo sapiens | G408 | TPLQQGIADYR | 1 | Bos taurus | G408 | TPLLQGIADYK | 1 | Mus musculus | H190 | -FHQGHHSVDT | 1 | Homo sapiens | H190 | HLLQDHVSVDT | 1 | Bos taurus | H190 | FTYQGHVSVDT | 1 | Mus musculus | H191 | FHQGHHSVDTA | 1 | Homo sapiens | H191 | LLQDHVSVDTM | 1 | Bos taurus | H191 | TYQGHVSVDTE | 1 | Mus musculus | L107 | MGQLALYLLAL | 2 | Homo sapiens, Bos taurus | L107 | GGSLALYLLAL | 1 | Mus musculus | L376 | ETQASLSGPYL | 1 | Homo sapiens | L376 | RTQASLSGPFL | 1 | Bos taurus | L376 | GTQASLSGPYL | 1 | Mus musculus | L381 | LSGPYLTSVMG | 1 | Homo sapiens | L381 | LSGPFLTSVLG | 1 | Bos taurus | L381 | LSGPYLTSVLG | 1 | Mus musculus | L397 | REFWQLLRDPN | 1 | Homo sapiens | L397 | REFWQVLRDPD | 1 | Bos taurus | L397 | REYWQLLRAPD | 1 | Mus musculus | L405 | DPNTPLLQGIA | 1 | Homo sapiens | L405 | DPDTPLQQGIA | 1 | Bos taurus | L405 | APDTPLLQGIA | 1 | Mus musculus | L406 | PNTPLLQGIAD | 1 | Homo sapiens | L406 | PDTPLQQGIAD | 1 | Bos taurus | L406 | PDTPLLQGIAD | 1 | Mus musculus | M288 | FQNPLMISQLL | 2 | Bos taurus, Mus musculus | M288 | FQNALMISQLL | 1 | Homo sapiens | N242 | EGHFGNVYSTP | 1 | Homo sapiens | N242 | EGYFGNVYSTP | 1 | Bos taurus | N242 | EGYFGNIYSTP | 1 | Mus musculus | P379 | ASLSGPYLTSV | 2 | Homo sapiens, Mus musculus | P379 | ASLSGPFLTSV | 1 | Bos taurus | Q104 | KPSMGQLALYL | 2 | Homo sapiens, Bos taurus | Q104 | KLSGGSLALYL | 1 | Mus musculus | Q156 | HTSYYQYGLGI | 1 | Homo sapiens | Q156 | RTSYYQYSLGI | 1 | Bos taurus | Q156 | NTNYYQYGLSI | 1 | Mus musculus | Q291 | ALMISQLLPVL | 1 | Homo sapiens | Q291 | PLMISQLLPVL | 1 | Bos taurus | Q291 | PLMISQLLPIL | 1 | Mus musculus | Q396 | EREFWQLLRDP | 1 | Homo sapiens | Q396 | EREFWQVLRDP | 1 | Bos taurus | Q396 | DREYWQLLRAP | 1 | Mus musculus | S153 | GHPHTSYYQYG | 1 | Homo sapiens | S153 | GHPRTSYYQYS | 1 | Bos taurus | S153 | GHPNTNYYQYG | 1 | Mus musculus | S245 | FGNVYSTPLAL | 2 | Homo sapiens, Bos taurus | S245 | FGNIYSTPLAL | 1 | Mus musculus | S375 | YETQASLSGPY | 1 | Homo sapiens | S375 | FRTQASLSGPF | 1 | Bos taurus | S375 | YGTQASLSGPY | 1 | Mus musculus | S377 | TQASLSGPYLT | 2 | Homo sapiens, Mus musculus | S377 | TQASLSGPFLT | 1 | Bos taurus | T152 | KGHPHTSYYQY | 1 | Homo sapiens | T152 | QGHPRTSYYQY | 1 | Bos taurus | T152 | EGHPNTNYYQY | 1 | Mus musculus | W395 | GEREFWQLLRD | 1 | Homo sapiens | W395 | GEREFWQVLRD | 1 | Bos taurus | W395 | GDREYWQLLRA | 1 | Mus musculus | W41 | QRLLPWMDRLS | 2 | Bos taurus, Mus musculus | W41 | QHLLPWMDRLS | 1 | Homo sapiens | Y155 | PHTSYYQYGLG | 1 | Homo sapiens | Y155 | PRTSYYQYSLG | 1 | Bos taurus | Y155 | PNTNYYQYGLS | 1 | Mus musculus | Y244 | HFGNVYSTPLA | 1 | Homo sapiens | Y244 | YFGNVYSTPLA | 1 | Bos taurus | Y244 | YFGNIYSTPLA | 1 | Mus musculus | Y380 | SLSGPYLTSVM | 1 | Homo sapiens | Y380 | SLSGPFLTSVL | 1 | Bos taurus | Y380 | SLSGPYLTSVL | 1 | Mus musculus |
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