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 APLF
Gene summary
Basic gene Info.Gene symbolAPLF
Gene nameaprataxin and PNKP like factor
CytomapUCSC genome browser: 2p13.3
Type of geneprotein-coding
DescriptionPNK and APTX-like FHA domain-containing proteinPNK and APTX-like FHA proteinXRCC1-interacting protein 1aprataxin and PNK-like factoraprataxin- and PNK-like factorapurinic-apyrimidinic endonuclease APLFzinc finger, CX5CX6HX5H motif containing 1
Modification date20141207
dbXrefs MIM : 611035
Ensembl : ENSG00000169621
HPRD : 09848
Vega : OTTHUMG00000129566
ProteinUniProt: Q8IW19
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APLF
BioGPS: 200558
PathwayNCI Pathway Interaction Database: APLF
Pathway Commons: APLF
ContextiHOP: APLF
ligand binding site mutation search in PubMed: APLF
UCL Cancer Institute: APLF
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0000737DNA catabolic process, endonucleolytic17396150
GO:0006974cellular response to DNA damage stimulus17396150
GO:0090305nucleic acid phosphodiester bond hydrolysis17396150

Ligand binding site mutations for APLF
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
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 APLF
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 APLF from PDB

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


Phenotype information for APLF
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for APLF
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 APLF go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2kqbAH392 H398
ZNZINC(2+)2kqdAH392 H398
ZNZINC(2+)2kuoAH392 H398
IIIPeptide ligand (TYR,ASP,GLU,SEP,TPO,ASP,GLU)5e50AR37 T59

Conservation information for LBS of APLF
Multiple alignments for Q8IW19 in multiple species
LBSAA sequence# speciesSpecies
C379VKRTSCMYGAN1Homo sapiens
C379VRRTACMYGAN1Mus musculus
C379VQRTSCMYGAN1Bos taurus
C385MYGANCYRKNP2Homo sapiens, Bos taurus
C385MYGANCYRRNP1Mus musculus
G28TVIGRGPLLGI2Homo sapiens, Mus musculus
G28TVIGRGPLLG-1Bos taurus
G382TSCMYGANCYR2Homo sapiens, Bos taurus
G382TACMYGANCYR1Mus musculus
H392RKNPVHFQHFS2Homo sapiens, Bos taurus
H392RRNPLHFQHFS1Mus musculus
H398FQHFSHPGDSD3Homo sapiens, Mus musculus, Bos taurus
H58RIKPIHTNPCF1Homo sapiens
H58RIKPIHRNPCF1Mus musculus
H58----LHRNPCY1Bos taurus
I33GPLLGITDKRV2Homo sapiens, Mus musculus
I33GPLLG------1Bos taurus
K36LGITDKRVSRR2Homo sapiens, Mus musculus
K36LG---------1Bos taurus
M380KRTSCMYGANC1Homo sapiens
M380RRTACMYGANC1Mus musculus
M380QRTSCMYGANC1Bos taurus
N384CMYGANCYRKN2Homo sapiens, Bos taurus
N384CMYGANCYRRN1Mus musculus
N431SCYRKNPQHKI2Homo sapiens, Bos taurus
N431SCYRKNPQHKM1Mus musculus
N60KPIHTNPCFYQ1Homo sapiens
N60KPIHRNPCFYQ1Mus musculus
N60--LHRNPCYYQ1Bos taurus
P29VIGRGPLLGIT2Homo sapiens, Mus musculus
P29VIGRGPLLG--1Bos taurus
R27ETVIGRGPLLG2Homo sapiens, Bos taurus
R27QTVIGRGPLLG1Mus musculus
R37GITDKRVSRRH2Homo sapiens, Mus musculus
R37G----------1Bos taurus
R387GANCYRKNPVH2Homo sapiens, Bos taurus
R387GANCYRRNPLH1Mus musculus
R40DKRVSRRHAIL2Homo sapiens, Mus musculus
R40-----------1Bos taurus
R429GASCYRKNPQH2Mus musculus, Bos taurus
R429GPSCYRKNPQH1Homo sapiens
S39TDKRVSRRHAI2Homo sapiens, Mus musculus
S39-----------1Bos taurus
S426CPYGASCYRKN2Mus musculus, Bos taurus
S426CPYGPSCYRKN1Homo sapiens
T34PLLGITDKRVS2Homo sapiens, Mus musculus
T34PLLG-------1Bos taurus
T59IKPIHTNPCFY1Homo sapiens
T59IKPIHRNPCFY1Mus musculus
T59---LHRNPCYY1Bos taurus
Y381RTSCMYGANCY2Homo sapiens, Bos taurus
Y381RTACMYGANCY1Mus musculus
Y386YGANCYRKNPV2Homo sapiens, Bos taurus
Y386YGANCYRRNPL1Mus musculus
Y423RPECPYGASCY2Mus musculus, Bos taurus
Y423RPECPYGPSCY1Homo sapiens

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