mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 PMM2
Gene summary
Basic gene Info.Gene symbolPMM2
Gene namephosphomannomutase 2
SynonymsCDG1|CDG1a|CDGS|PMI|PMI1|PMM 2
CytomapUCSC genome browser: 16p13
Type of geneprotein-coding
RefGenesNM_000303.2,
Descriptionphosphomannose isomerase 1
Modification date20141222
dbXrefs MIM : 601785
HGNC : HGNC
Ensembl : ENSG00000140650
HPRD : 03472
Vega : OTTHUMG00000129697
ProteinUniProt: O15305
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PMM2
BioGPS: 5373
PathwayNCI Pathway Interaction Database: PMM2
KEGG: PMM2
REACTOME: PMM2
Pathway Commons: PMM2
ContextiHOP: PMM2
ligand binding site mutation search in PubMed: PMM2
UCL Cancer Institute: PMM2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for PMM2
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.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K109A108TCOAD1
K109K109ESTAD1
F221E219QSTAD1
K109A108VUCEC1
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 PMM2
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
F221E219Q-1.4080168
K109A108T-1.0808036
K109A108V-0.75366798
K109K109E-0.75320414
(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 PMM2 from PDB

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Differential gene expression and gene-gene network for PMM2
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 PMM2 and the right PPI network was created from samples without mutations in the LBS of PMM2. 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 PMM2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0349653Congenital disorder of glycosylation type 1A34Biomarker, GeneticVariation
umls:C3714756Intellectual Disability1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs
98707A108VLikely pathogenicGermlineGeneReviews:NBK1110
MedGen:C0349653
OMIM:212065
Orphanet:ORPHA79318
SNOMED CT:277893002
MedGen:CN221809

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Pharmacological information for PMM2
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 PMM2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
GLYGLYCINE RESIDUE2amyAF221
GLYGLYCINE RESIDUE2q4rAF221
GLYGLYCINE RESIDUE2amyAK109
GLYGLYCINE RESIDUE2q4rAK109


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Conservation information for LBS of PMM2
Multiple alignments for O15305 in multiple species
LBSAA sequence# speciesSpecies
D223HEIFTDPRTVG2Mus musculus, Bos taurus
D223HEIFTDPRTMG1Homo sapiens
D223HEIFADERTVG1Caenorhabditis elegans
D223YEIYSDPRTIS1Drosophila melanogaster
D223YEIYESPKTIG1Arabidopsis thaliana
D223YEIFESDRTIG1Oryza sativa subsp. japonica
D223YEIFVDERTIG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D223YEIFVDPRTIG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F221NDHEIFTDPRT3Homo sapiens, Mus musculus, Bos taurus
F221NDHEIFADERT1Caenorhabditis elegans
F221NDYEIYSDPRT1Drosophila melanogaster
F221NDYEIYESPKT1Arabidopsis thaliana
F221NDYEIFESDRT1Oryza sativa subsp. japonica
F221NDYEIFVDERT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F221NDYEIFVDPRT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G228DPRTMGYSVTA1Homo sapiens
G228DERTVGHTVEG1Caenorhabditis elegans
G228DPRTISHRVYT1Drosophila melanogaster
G228DPRTVGYTVTA1Mus musculus
G228DPRTVGYTVAA1Bos taurus
G228SPKTIGHSVTS1Arabidopsis thaliana
G228SDRTIGHTVTS1Oryza sativa subsp. japonica
G228DERTIGHSVQS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G228DPRTIGHSVTN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K109LSYIAKIKLPK2Homo sapiens, Bos taurus
K109LHYIADLDIPI2Arabidopsis thaliana, Oryza sativa subsp. japonica
K109LRYMSDIQLPV1Caenorhabditis elegans
K109LRYLSELDVPI1Drosophila melanogaster
K109LSYIANIKLPK1Mus musculus
K109LRYLSEIDLPK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K109LHYIADLDIPV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K202ND-GYKTIYFF1Homo sapiens
K202PD--FDTIHFF1Caenorhabditis elegans
K202AHYKFKEIHFF1Drosophila melanogaster
K202HA-GYKTIYFF1Mus musculus
K202KD-GYKTIYFF1Bos taurus
K202D---FSEIHFF1Arabidopsis thaliana
K202E---FQEIHFF1Oryza sativa subsp. japonica
K202KD-GFKEIHFF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K202KE-GFDTIHFF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R225IFTDPRTVGYT2Mus musculus, Bos taurus
R225IFTDPRTMGYS1Homo sapiens
R225IFADERTVGHT1Caenorhabditis elegans
R225IYSDPRTISHR1Drosophila melanogaster
R225IYESPKTIGHS1Arabidopsis thaliana
R225IFESDRTIGHT1Oryza sativa subsp. japonica
R225IFVDERTIGHS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R225IFVDPRTIGHS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S105INYCLSYIAKI2Homo sapiens, Bos taurus
S105INFTLHYIADL2Arabidopsis thaliana, Oryza sativa subsp. japonica
S105INFALRYMSDI1Caenorhabditis elegans
S105INFVLRYLSEL1Drosophila melanogaster
S105INYCLSYIANI1Mus musculus
S105AVFILRYLSEI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S105VNFCLHYIADL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T222DHEIFTDPRTV2Mus musculus, Bos taurus
T222DHEIFTDPRTM1Homo sapiens
T222DHEIFADERTV1Caenorhabditis elegans
T222DYEIYSDPRTI1Drosophila melanogaster
T222DYEIYESPKTI1Arabidopsis thaliana
T222DYEIFESDRTI1Oryza sativa subsp. japonica
T222DYEIFVDERTI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T222DYEIFVDPRTI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T226FTDPRTVGYTV2Mus musculus, Bos taurus
T226FTDPRTMGYSV1Homo sapiens
T226FADERTVGHTV1Caenorhabditis elegans
T226YSDPRTISHRV1Drosophila melanogaster
T226YESPKTIGHSV1Arabidopsis thaliana
T226FESDRTIGHTV1Oryza sativa subsp. japonica
T226FVDERTIGHSV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T226FVDPRTIGHSV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y102QDLINYCLSYI3Homo sapiens, Mus musculus, Bos taurus
Y102QELINFALRYM1Caenorhabditis elegans
Y102KRFINFVLRYL1Drosophila melanogaster
Y102KELINFTLHYI1Arabidopsis thaliana
Y102KEFINFTLHYI1Oryza sativa subsp. japonica
Y102NKLAVFILRYL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y102QKLVNFCLHYI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y106NYCLSYIAKIK2Homo sapiens, Bos taurus
Y106NFTLHYIADLD2Arabidopsis thaliana, Oryza sativa subsp. japonica
Y106NFALRYMSDIQ1Caenorhabditis elegans
Y106NFVLRYLSELD1Drosophila melanogaster
Y106NYCLSYIANIK1Mus musculus
Y106VFILRYLSEID1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y106NFCLHYIADLD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y201END-GYKTIYF1Homo sapiens
Y201VPD--FDTIHF1Caenorhabditis elegans
Y201EAHYKFKEIHF1Drosophila melanogaster
Y201EHA-GYKTIYF1Mus musculus
Y201EKD-GYKTIYF1Bos taurus
Y201ED---FSEIHF1Arabidopsis thaliana
Y201EE---FQEIHF1Oryza sativa subsp. japonica
Y201EKD-GFKEIHF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y201EKE-GFDTIHF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)


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