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mutLBSgeneDB |
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| Gene summary for GIF |
 Gene summary |
| Basic gene Info. | Gene symbol | GIF |
| Gene name | gastric intrinsic factor (vitamin B synthesis) | |
| Synonyms | IF|IFMH|INF|TCN3 | |
| Cytomap | UCSC genome browser: 11q13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_005142.2, | |
| Description | gastric intrinsic factorintrinsic factor | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 609342 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000134812 | ||
| HPRD : 02024 | ||
| Vega : OTTHUMG00000167399 | ||
| Protein | UniProt: P27352 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_GIF | |
| BioGPS: 2694 | ||
| Pathway | NCI Pathway Interaction Database: GIF | |
| KEGG: GIF | ||
| REACTOME: GIF | ||
| Pathway Commons: GIF | ||
| Context | iHOP: GIF | |
| ligand binding site mutation search in PubMed: GIF | ||
| UCL Cancer Institute: GIF | ||
| 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 GIF |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | S365 | S365Y | UCEC | 2 | F388 | L389I | COAD | 1 | Y133 | P135H | GBM | 1 | P394 | P394T | LUAD | 1 | L94 | L94I | LUSC | 1 | G367 | G367S | SKCM | 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 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 |
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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 | G367 | G367S | -1.2968134 | L94 | L94I | -1.1371842 | P394 | P394T | -0.92412238 | F388 | L389I | -0.81015962 | S365 | S365Y | -0.76171448 | Y133 | P135H | -0.51884612 |
| (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 ID | PDB title | PDB structure | 2PMV | Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution |  |
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| 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) |
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| Phenotype information for GIF |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1394891 | Intrinsic Factor Deficiency | 2 | Biomarker, GeneticVariation |
| umls:C0036341 | Schizophrenia | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| 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. |
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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 GIF go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | B12 | COBALAMIN | 3kq4 | A | L94 Y133 S365 G367 F388 | B12 | COBALAMIN | 3kq4 | C | L94 Y133 S365 G367 F388 | B12 | COBALAMIN | 3kq4 | E | L94 Y133 S365 G367 F388 |
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| Conservation information for LBS of GIF |
| Multiple alignments for P27352 in multiple species |
| LBS | AA sequence | # species | Species | D171 | SPFNVDTGAMA | 1 | Homo sapiens | D171 | SPFNTDTGAMV | 1 | Canis lupus familiaris | D171 | SPFNVDTGAVA | 1 | Mus musculus | D171 | SPFSVDTGAVA | 1 | Rattus norvegicus | D222 | DGIIGDIYSTG | 2 | Mus musculus, Rattus norvegicus | D222 | NGIIGDIYSTG | 1 | Homo sapiens | D222 | NGIIGDVYSTG | 1 | Canis lupus familiaris | E397 | VTPLNEGVADY | 1 | Homo sapiens | E397 | KTPLNEGVADY | 1 | Canis lupus familiaris | E397 | KTPLDEGVAYY | 1 | Mus musculus | E397 | KTPLGEGVAYY | 1 | Rattus norvegicus | F388 | KTYWEFLSGKT | 2 | Mus musculus, Rattus norvegicus | F388 | KTYWQFLSGVT | 1 | Homo sapiens | F388 | RTYWQFLSGKT | 1 | Canis lupus familiaris | G367 | TMTSWGLVVSS | 2 | Homo sapiens, Canis lupus familiaris | G367 | TMTSWGLIVSS | 2 | Mus musculus, Rattus norvegicus | G398 | TPLNEGVADYI | 1 | Homo sapiens | G398 | TPLNEGVADYT | 1 | Canis lupus familiaris | G398 | TPLDEGVAYYI | 1 | Mus musculus | G398 | TPLGEGVAYYI | 1 | Rattus norvegicus | L228 | IYSTGLAMQAL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L228 | VYSTGLAMQAL | 1 | Canis lupus familiaris | L368 | MTSWGLVVSSI | 2 | Homo sapiens, Canis lupus familiaris | L368 | MTSWGLIVSSI | 2 | Mus musculus, Rattus norvegicus | L395 | SGVTPLNEGVA | 1 | Homo sapiens | L395 | SGKTPLNEGVA | 1 | Canis lupus familiaris | L395 | SGKTPLDEGVA | 1 | Mus musculus | L395 | SGKTPLGEGVA | 1 | Rattus norvegicus | L94 | IGQLGLTIMAL | 1 | Homo sapiens | L94 | VGQLALTIMAL | 1 | Canis lupus familiaris | L94 | SGQLALTVMAL | 1 | Mus musculus | L94 | NGQLALTIMAL | 1 | Rattus norvegicus | N396 | GVTPLNEGVAD | 1 | Homo sapiens | N396 | GKTPLNEGVAD | 1 | Canis lupus familiaris | N396 | GKTPLDEGVAY | 1 | Mus musculus | N396 | GKTPLGEGVAY | 1 | Rattus norvegicus | P394 | LSGVTPLNEGV | 1 | Homo sapiens | P394 | LSGKTPLNEGV | 1 | Canis lupus familiaris | P394 | LSGKTPLDEGV | 1 | Mus musculus | P394 | LSGKTPLGEGV | 1 | Rattus norvegicus | Q270 | PMSIAQILPSL | 4 | Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus | Q387 | HKTYWEFLSGK | 2 | Mus musculus, Rattus norvegicus | Q387 | HKTYWQFLSGV | 1 | Homo sapiens | Q387 | DRTYWQFLSGK | 1 | Canis lupus familiaris | S130 | PNAEASAFYGP | 1 | Homo sapiens | S130 | PSAPAWTFYGP | 1 | Canis lupus familiaris | S130 | PGAESSAFYGP | 1 | Mus musculus | S130 | LGAESSSFYGP | 1 | Rattus norvegicus | S225 | IGDIYSTGLAM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S225 | IGDVYSTGLAM | 1 | Canis lupus familiaris | S365 | ETTMTSWGLIV | 2 | Mus musculus, Rattus norvegicus | S365 | ETTMTSWGLVV | 1 | Homo sapiens | S365 | VTTMTSWGLVV | 1 | Canis lupus familiaris | T364 | FETTMTSWGLI | 2 | Mus musculus, Rattus norvegicus | T364 | FETTMTSWGLV | 1 | Homo sapiens | T364 | FVTTMTSWGLV | 1 | Canis lupus familiaris | V369 | TSWGLVVSSIN | 2 | Homo sapiens, Canis lupus familiaris | V369 | TSWGLIVSSIN | 2 | Mus musculus, Rattus norvegicus | V370 | SWGLVVSSINN | 2 | Homo sapiens, Canis lupus familiaris | V370 | SWGLIVSSINN | 2 | Mus musculus, Rattus norvegicus | V380 | NIAENVNHKTY | 2 | Homo sapiens, Mus musculus | V380 | NIAESVHDRTY | 1 | Canis lupus familiaris | V380 | NIAENVKHKTY | 1 | Rattus norvegicus | W366 | TTMTSWGLVVS | 2 | Homo sapiens, Canis lupus familiaris | W366 | TTMTSWGLIVS | 2 | Mus musculus, Rattus norvegicus | W386 | NHKTYWQFLSG | 1 | Homo sapiens | W386 | HDRTYWQFLSG | 1 | Canis lupus familiaris | W386 | NHKTYWEFLSG | 1 | Mus musculus | W386 | KHKTYWEFLSG | 1 | Rattus norvegicus | Y133 | EASAFYGPSLA | 1 | Homo sapiens | Y133 | PAWTFYGPSLA | 1 | Canis lupus familiaris | Y133 | ESSAFYGPGLA | 1 | Mus musculus | Y133 | ESSSFYGPALA | 1 | Rattus norvegicus | Y224 | IIGDIYSTGLA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y224 | IIGDVYSTGLA | 1 | Canis lupus familiaris | Y385 | VNHKTYWQFLS | 1 | Homo sapiens | Y385 | VHDRTYWQFLS | 1 | Canis lupus familiaris | Y385 | VNHKTYWEFLS | 1 | Mus musculus | Y385 | VKHKTYWEFLS | 1 | Rattus norvegicus | Y7 | AWFALYLLSLL | 1 | Homo sapiens | Y7 | AWFSLHLLHLL | 1 | Canis lupus familiaris | Y7 | AWLTLYLLSVL | 1 | Mus musculus | Y7 | AWLSFYLLNVL | 1 | Rattus norvegicus |
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