mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for TCN1

Gene summary

Basic gene Info.	Gene symbol	TCN1
	Gene name	transcobalamin I (vitamin B12 binding protein, R binder family)
	Synonyms	HC\|TC-1\|TC1\|TCI
	Cytomap	UCSC genome browser: 11q11-q12
	Type of gene	protein-coding
	RefGenes	NM_001062.3,
	Description	haptocorinhaptocorrinprotein Rtranscobalamin-1
	Modification date	20141207
dbXrefs	MIM : 189905
	HGNC : HGNC
	Ensembl : ENSG00000134827
	HPRD : 01795
	Vega : OTTHUMG00000167400
Protein	UniProt: P20061 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TCN1
	BioGPS: 6947
Pathway	NCI Pathway Interaction Database: TCN1
	KEGG: TCN1
	REACTOME: TCN1
	Pathway Commons: TCN1
Context	iHOP: TCN1
	ligand binding site mutation search in PubMed: TCN1
	UCL Cancer Institute: TCN1
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 TCN1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
E94	E94Q	BLCA	1
T142	P140T	LUSC	1
D186	G188D	SKCM	1
D370	T371A	STAD	1
G93	S92L	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.

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Protein structure related information for TCN1

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
G93	S92L	0.74788081
D370	T371A	-1.338272
E94	E94Q	-1.0670325
T142	P140T	-0.78440296
D186	G188D	-0.62690887

(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 TCN1 from PDB

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Differential gene expression and gene-gene network for TCN1

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)

* Left PPI network was created from samples with mutations in the LBS of TCN1 and the right PPI network was created from samples without mutations in the LBS of TCN1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

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Phenotype information for TCN1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0002888	Anemia, Megaloblastic	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TCN1

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.