mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	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 CAMK2D

Gene summary

Basic gene Info.	Gene symbol	CAMK2D
	Gene name	calcium/calmodulin-dependent protein kinase II delta
	Synonyms	CAMKD
	Cytomap	UCSC genome browser: 4q26
	Type of gene	protein-coding
	RefGenes	NM_001221.3, NM_172114.1,NM_172115.2,NM_172127.2,NM_172128.2, NM_172129.1,
	Description	CaM kinase II delta subunitCaM-kinase II delta chainCaMK-II delta subunitcaM kinase II subunit deltacaMK-II subunit deltacalcium/calmodulin-dependent protein kinase (CaM kinase) II deltacalcium/calmodulin-dependent protein kinase type II delta chain
	Modification date	20141207
dbXrefs	MIM : 607708
	HGNC : HGNC
	Ensembl : ENSG00000145349
	HPRD : 09653
	Vega : OTTHUMG00000132910
Protein	UniProt: Q13557 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CAMK2D
	BioGPS: 817
Pathway	NCI Pathway Interaction Database: CAMK2D
	KEGG: CAMK2D
	REACTOME: CAMK2D
	Pathway Commons: CAMK2D
Context	iHOP: CAMK2D
	ligand binding site mutation search in PubMed: CAMK2D
	UCL Cancer Institute: CAMK2D
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0003254	regulation of membrane depolarization	22514276
GO:0006468	protein phosphorylation	17179159
GO:0018105	peptidyl-serine phosphorylation	22514276
GO:0018107	peptidyl-threonine phosphorylation	22514276
GO:0046777	protein autophosphorylation	22514276
GO:0051259	protein oligomerization	20668654
GO:1901897	regulation of relaxation of cardiac muscle	23283722
GO:1902306	negative regulation of sodium ion transmembrane transport	22514276
GO:2000650	negative regulation of sodium ion transmembrane transporter activity	22514276

Top

Ligand binding site mutations for CAMK2D

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
K22	A24T	HNSC	1
V28	V28L	LUAD	1
V28	S26L	LUSC	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.

Top

Protein structure related information for CAMK2D

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
K22	A24T	-0.87960345
V28	V28L	-0.37639201
V28	S26L	-0.003823637

(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 CAMK2D from PDB

Top

Differential gene expression and gene-gene network for CAMK2D

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 CAMK2D and the right PPI network was created from samples without mutations in the LBS of CAMK2D. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for CAMK2D

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0151744	Myocardial Ischemia	1	Biomarker
umls:C0032460	Polycystic Ovary Syndrome	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

Top

Pharmacological information for CAMK2D

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Experimental	DB07853	[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE	Small molecule
Experimental	DB08039	(3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CAMK2D go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
GVD		[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE	2vn9	A	K22 V28
GVD		[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE	2vn9	B	K22 V28
K88		(3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE	2wel	A	V28

Top

Conservation information for LBS of CAMK2D

Multiple alignments for Q13557 in multiple species

LBS	AA sequence	# species	Species
A156	AAVKLADFGLA	7	Homo sapiens, Drosophila melanogaster, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
A41	TGQEYAAKIIN	6	Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
A41	TGFEFAAKIIN	1	Drosophila melanogaster
D157	AVKLADFGLAI	7	Homo sapiens, Drosophila melanogaster, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
D91	HYLVFDLVTGG	7	Homo sapiens, Drosophila melanogaster, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
F90	FHYLVFDLVTG	5	Homo sapiens, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
F90	YHYLVFDLVTG	1	Drosophila melanogaster
F90	VHYLVFDLVTG	1	Danio rerio
G21	LFEELGKGAFS	5	Homo sapiens, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
G21	IKEELGKGAFS	1	Drosophila melanogaster
G21	LYEELGKGAFS	1	Danio rerio
K22	FEELGKGAFSV	5	Homo sapiens, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
K22	KEELGKGAFSI	1	Drosophila melanogaster
K22	YEELGKGAFSV	1	Danio rerio
K43	QEYAAKIINTK	6	Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
K43	FEFAAKIINTK	1	Drosophila melanogaster
L20	QLFEELGKGAF	5	Homo sapiens, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
L20	DIKEELGKGAF	1	Drosophila melanogaster
L20	QLYEELGKGAF	1	Danio rerio
L92	YLVFDLVTGGE	7	Homo sapiens, Drosophila melanogaster, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
V28	GAFSVVRRCMK	6	Homo sapiens, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus
V28	GAFSIVKRCVQ	1	Drosophila melanogaster
V93	LVFDLVTGGEL	7	Homo sapiens, Drosophila melanogaster, Danio rerio, Gallus gallus, Rattus norvegicus, Bos taurus, Mus musculus