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 GM2A

Gene summary

Basic gene Info.	Gene symbol	GM2A
	Gene name	GM2 ganglioside activator
	Synonyms	GM2-AP\|SAP-3
	Cytomap	UCSC genome browser: 5q33.1
	Type of gene	protein-coding
	RefGenes	NM_000405.4, NM_001167607.1,
	Description	cerebroside sulfate activator proteinganglioside GM2 activatorshingolipid activator protein 3sphingolipid activator protein 3
	Modification date	20141207
dbXrefs	MIM : 613109
	HGNC : HGNC
	Ensembl : ENSG00000196743
	HPRD : 02034
	Vega : OTTHUMG00000130124
Protein	UniProt: P17900 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GM2A
	BioGPS: 2760
Pathway	NCI Pathway Interaction Database: GM2A
	KEGG: GM2A
	REACTOME: GM2A
	Pathway Commons: GM2A
Context	iHOP: GM2A
	ligand binding site mutation search in PubMed: GM2A
	UCL Cancer Institute: GM2A
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 GM2A

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
L129	R130C	COAD	1
I119	P120S	SKCM	1
L174	S176N	SKCM	1
L129	R130H	STAD	1
F111	C112Y	STAD	1
F108	C106R	UCEC	1
L76,T72	V74I	UCEC	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 GM2A

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
I119	P120S	-1.1845658
L129	R130H	-1.0235692
F111	C112Y	-0.98398642
L174	S176N	-0.96704852
L129	R130C	-0.7309664
L76	V74I	-0.42989042
T72	V74I	-0.42989042
F108	C106R	-0.079029327

(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 GM2A from PDB

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Differential gene expression and gene-gene network for GM2A

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 GM2A and the right PPI network was created from samples without mutations in the LBS of GM2A. 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 GM2A

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0268275	Tay-Sachs Disease, AB Variant	3	Biomarker, GeneticVariation
umls:C0039373	Tay-Sachs Disease	2	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for GM2A

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.

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Experimental	DB02261	Platelet Activating Factor	Small molecule
Approved	DB02325	Isopropyl Alcohol	Small molecule
Experimental	DB03633	Lpc-Ether	Small molecule
Experimental	DB04660	Choline alfoscerate	Small molecule
Experimental	DB08231	MYRISTIC ACID	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GM2A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
ACT		ACETATE	1tjj	A	F111
LPE		1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE	1tjj	A	F111
LPE		1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE	1tjj	B	F111
LPE		1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE	1tjj	C	F111
LP3		(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE	2ag2	A	F111
LP3		(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE	2ag2	B	F111
LP3		(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE	2ag4	A	F111
LP3		(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE	2ag4	B	F111

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Conservation information for LBS of GM2A

Multiple alignments for P17900 in multiple species

LBS

AA sequence

# species

Species