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 PLEKHA4

Gene summary

Basic gene Info.	Gene symbol	PLEKHA4
	Gene name	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4
	Synonyms	PEPP1
	Cytomap	UCSC genome browser: 19q13.33
	Type of gene	protein-coding
	RefGenes	NM_001161354.1, NM_020904.2,
	Description	PEPP-1PH domain-containing family A member 4phosphoinositol 3-phosphate binding protein-1phosphoinositol 3-phosphate-binding PH domain protein 1phosphoinositol 3-phosphate-binding protein 1pleckstrin homology domain-containing family A member 4
	Modification date	20141207
dbXrefs	MIM : 607769
	HGNC : HGNC
	Ensembl : ENSG00000105559
	HPRD : 09683
	Vega : OTTHUMG00000183329
Protein	UniProt: Q9H4M7 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLEKHA4
	BioGPS: 57664
Pathway	NCI Pathway Interaction Database: PLEKHA4
	KEGG: PLEKHA4
	REACTOME: PLEKHA4
	Pathway Commons: PLEKHA4
Context	iHOP: PLEKHA4
	ligand binding site mutation search in PubMed: PLEKHA4
	UCL Cancer Institute: PLEKHA4
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 PLEKHA4

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
R129	M128T	COAD	1
R129	G127C	LUAD	1
D65	D65Y	STAD	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 PLEKHA4

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.

LBS	AAchange of nsSNV	Relative stability change
R129	M128T	-1.3951867
R129	G127C	-0.74014655
D65	D65Y	-0.49165252

(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 PLEKHA4 from PDB

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Differential gene expression and gene-gene network for PLEKHA4

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 PLEKHA4 and the right PPI network was created from samples without mutations in the LBS of PLEKHA4. 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 PLEKHA4

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for PLEKHA4

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.