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 PHF19
Gene summary
Basic gene Info.Gene symbolPHF19
Gene namePHD finger protein 19
SynonymsMTF2L1|PCL3|TDRD19B
CytomapUCSC genome browser: 9q33.2
Type of geneprotein-coding
RefGenesNM_001009936.2,
NM_001286840.1,NM_001286842.1,NM_001286843.1,NM_015651.2,
NR_104601.1,
Descriptionpolycomb like 3polycomb-like protein 3tudor domain containing 19B
Modification date20141207
dbXrefs MIM : 609740
HGNC : HGNC
Ensembl : ENSG00000119403
HPRD : 17846
Vega : OTTHUMG00000020577
ProteinUniProt: Q5T6S3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PHF19
BioGPS: 26147
PathwayNCI Pathway Interaction Database: PHF19
KEGG: PHF19
REACTOME: PHF19
Pathway Commons: PHF19
ContextiHOP: PHF19
ligand binding site mutation search in PubMed: PHF19
UCL Cancer Institute: PHF19
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 PHF19
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
G94E96KOV1
L47V46ASTAD1
E75E75KUCEC1
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 PHF19
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
E75E75K-1.5736775
L47V46A-1.3407652
G94E96K-1.0485285
(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 PHF19 from PDB

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Differential gene expression and gene-gene network for PHF19
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 PHF19 and the right PPI network was created from samples without mutations in the LBS of PHF19. 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 PHF19
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for PHF19
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 PHF19 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (ALA,THR,GLY,GLY,VAL,LYS,LYS,PRO,HIS,ARG,TYR)4bd3AL47 E75 G94


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Conservation information for LBS of PHF19
Multiple alignments for Q5T6S3 in multiple species
LBSAA sequence# speciesSpecies
D52LCRWTDGLYYL2Homo sapiens, Mus musculus
D52KC--NDGRFYL1Drosophila melanogaster
D76LVTFEDNSKYW2Homo sapiens, Mus musculus
D76LIRFDDQSEQW1Drosophila melanogaster
E75CLVTFEDNSKY2Homo sapiens, Mus musculus
E75YLIRFDDQSEQ1Drosophila melanogaster
F74SCLVTFEDNSK2Homo sapiens, Mus musculus
F74QYLIRFDDQSE1Drosophila melanogaster
G53CRWTDGLYYLG2Homo sapiens, Mus musculus
G53C--NDGRFYLG1Drosophila melanogaster
G94---VPGEEPKC2Homo sapiens, Mus musculus
G94TTESTNTSPSG1Drosophila melanogaster
H89WKDIQHAG---2Homo sapiens, Mus musculus
H89PDKLRKLGGGS1Drosophila melanogaster
L47EGQYVLCRWTD1Homo sapiens
L47EDVFIKC--ND1Drosophila melanogaster
L47EGQFVLCRWTD1Mus musculus
L54RWTDGLYYLGK2Homo sapiens, Mus musculus
L54--NDGRFYLGT1Drosophila melanogaster
Q88LWKDIQHAG--2Homo sapiens, Mus musculus
Q88EPDKLRKLGGG1Drosophila melanogaster
R49QYVLCRWTDGL1Homo sapiens
R49VFIKC--NDGR1Drosophila melanogaster
R49QFVLCRWTDGL1Mus musculus
S78TFEDNSKYWVL2Homo sapiens, Mus musculus
S78RFDDQSEQWCE1Drosophila melanogaster
V92-----VPGEEP2Homo sapiens, Mus musculus
V92ASTTESTNTSP1Drosophila melanogaster
W50YVLCRWTDGLY1Homo sapiens
W50FIKC--NDGRF1Drosophila melanogaster
W50FVLCRWTDGLY1Mus musculus
Y55WTDGLYYLGKI2Homo sapiens, Mus musculus
Y55-NDGRFYLGTI1Drosophila melanogaster
Y56TDGLYYLGKIK2Homo sapiens, Mus musculus
Y56NDGRFYLGTI-1Drosophila melanogaster
Y80EDNSKYWVLWK2Homo sapiens, Mus musculus
Y80DDQSEQWCEPD1Drosophila melanogaster


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