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 GIF
Gene summary
Basic gene Info.Gene symbolGIF
Gene namegastric intrinsic factor (vitamin B synthesis)
CytomapUCSC genome browser: 11q13
Type of geneprotein-coding
Descriptiongastric intrinsic factorintrinsic factor
Modification date20141207
dbXrefs MIM : 609342
Ensembl : ENSG00000134812
HPRD : 02024
Vega : OTTHUMG00000167399
ProteinUniProt: P27352
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GIF
BioGPS: 2694
PathwayNCI Pathway Interaction Database: GIF
Pathway Commons: GIF
ContextiHOP: GIF
ligand binding site mutation search in PubMed: GIF
UCL Cancer Institute: GIF
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for GIF

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for GIF
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.
LBSAAchange of nsSNVRelative stability change
(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 GIF from PDB
PDB IDPDB titlePDB structure
2PMVCrystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution

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


Phenotype information for GIF
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1394891Intrinsic Factor Deficiency2Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for GIF
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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GIF go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
B12COBALAMIN3kq4AL94 Y133 S365 G367 F388
B12COBALAMIN3kq4CL94 Y133 S365 G367 F388
B12COBALAMIN3kq4EL94 Y133 S365 G367 F388

Conservation information for LBS of GIF
Multiple alignments for P27352 in multiple species
LBSAA sequence# speciesSpecies
D171SPFNVDTGAMA1Homo sapiens
D171SPFNTDTGAMV1Canis lupus familiaris
D171SPFNVDTGAVA1Mus musculus
D171SPFSVDTGAVA1Rattus norvegicus
D222DGIIGDIYSTG2Mus musculus, Rattus norvegicus
D222NGIIGDIYSTG1Homo sapiens
D222NGIIGDVYSTG1Canis lupus familiaris
E397VTPLNEGVADY1Homo sapiens
E397KTPLNEGVADY1Canis lupus familiaris
E397KTPLDEGVAYY1Mus musculus
E397KTPLGEGVAYY1Rattus norvegicus
F388KTYWEFLSGKT2Mus musculus, Rattus norvegicus
F388KTYWQFLSGVT1Homo sapiens
F388RTYWQFLSGKT1Canis lupus familiaris
G367TMTSWGLVVSS2Homo sapiens, Canis lupus familiaris
G367TMTSWGLIVSS2Mus musculus, Rattus norvegicus
G398TPLNEGVADYI1Homo sapiens
G398TPLNEGVADYT1Canis lupus familiaris
G398TPLDEGVAYYI1Mus musculus
G398TPLGEGVAYYI1Rattus norvegicus
L228IYSTGLAMQAL3Homo sapiens, Mus musculus, Rattus norvegicus
L228VYSTGLAMQAL1Canis lupus familiaris
L368MTSWGLVVSSI2Homo sapiens, Canis lupus familiaris
L368MTSWGLIVSSI2Mus musculus, Rattus norvegicus
L395SGVTPLNEGVA1Homo sapiens
L395SGKTPLNEGVA1Canis lupus familiaris
L395SGKTPLDEGVA1Mus musculus
L395SGKTPLGEGVA1Rattus norvegicus
L94IGQLGLTIMAL1Homo sapiens
L94VGQLALTIMAL1Canis lupus familiaris
L94SGQLALTVMAL1Mus musculus
L94NGQLALTIMAL1Rattus norvegicus
N396GVTPLNEGVAD1Homo sapiens
N396GKTPLNEGVAD1Canis lupus familiaris
N396GKTPLDEGVAY1Mus musculus
N396GKTPLGEGVAY1Rattus norvegicus
P394LSGVTPLNEGV1Homo sapiens
P394LSGKTPLNEGV1Canis lupus familiaris
P394LSGKTPLDEGV1Mus musculus
P394LSGKTPLGEGV1Rattus norvegicus
Q270PMSIAQILPSL4Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
Q387HKTYWEFLSGK2Mus musculus, Rattus norvegicus
Q387HKTYWQFLSGV1Homo sapiens
Q387DRTYWQFLSGK1Canis lupus familiaris
S130PNAEASAFYGP1Homo sapiens
S130PSAPAWTFYGP1Canis lupus familiaris
S130PGAESSAFYGP1Mus musculus
S130LGAESSSFYGP1Rattus norvegicus
S225IGDIYSTGLAM3Homo sapiens, Mus musculus, Rattus norvegicus
S225IGDVYSTGLAM1Canis lupus familiaris
S365ETTMTSWGLIV2Mus musculus, Rattus norvegicus
S365ETTMTSWGLVV1Homo sapiens
S365VTTMTSWGLVV1Canis lupus familiaris
T364FETTMTSWGLI2Mus musculus, Rattus norvegicus
T364FETTMTSWGLV1Homo sapiens
T364FVTTMTSWGLV1Canis lupus familiaris
V369TSWGLVVSSIN2Homo sapiens, Canis lupus familiaris
V369TSWGLIVSSIN2Mus musculus, Rattus norvegicus
V370SWGLVVSSINN2Homo sapiens, Canis lupus familiaris
V370SWGLIVSSINN2Mus musculus, Rattus norvegicus
V380NIAENVNHKTY2Homo sapiens, Mus musculus
V380NIAESVHDRTY1Canis lupus familiaris
V380NIAENVKHKTY1Rattus norvegicus
W366TTMTSWGLVVS2Homo sapiens, Canis lupus familiaris
W366TTMTSWGLIVS2Mus musculus, Rattus norvegicus
W386NHKTYWQFLSG1Homo sapiens
W386HDRTYWQFLSG1Canis lupus familiaris
W386NHKTYWEFLSG1Mus musculus
W386KHKTYWEFLSG1Rattus norvegicus
Y133EASAFYGPSLA1Homo sapiens
Y133PAWTFYGPSLA1Canis lupus familiaris
Y133ESSAFYGPGLA1Mus musculus
Y133ESSSFYGPALA1Rattus norvegicus
Y224IIGDIYSTGLA3Homo sapiens, Mus musculus, Rattus norvegicus
Y224IIGDVYSTGLA1Canis lupus familiaris
Y385VNHKTYWQFLS1Homo sapiens
Y385VHDRTYWQFLS1Canis lupus familiaris
Y385VNHKTYWEFLS1Mus musculus
Y385VKHKTYWEFLS1Rattus norvegicus
Y7AWFALYLLSLL1Homo sapiens
Y7AWFSLHLLHLL1Canis lupus familiaris
Y7AWLTLYLLSVL1Mus musculus
Y7AWLSFYLLNVL1Rattus norvegicus

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