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 MMAB

Gene summary

Basic gene Info.	Gene symbol	MMAB
	Gene name	methylmalonic aciduria (cobalamin deficiency) cblB type
	Synonyms	ATR\|CFAP23\|cblB\|cob
	Cytomap	UCSC genome browser: 12q24
	Type of gene	protein-coding
	RefGenes	NM_052845.3, NR_038118.1,
	Description	ATP:cob(I)alamin adenosyltransferaseATP:corrinoid adenosyltransferaseaquocob(I)alamin vitamin B12s adenosyltransferasecilia and flagella associated protein 23cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrialmethylmalonic aciduria type
	Modification date	20141219
dbXrefs	MIM : 607568
	HGNC : HGNC
	Ensembl : ENSG00000139428
	HPRD : 07398
	Vega : OTTHUMG00000169255
Protein	UniProt: Q96EY8 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MMAB
	BioGPS: 326625
Pathway	NCI Pathway Interaction Database: MMAB
	KEGG: MMAB
	REACTOME: MMAB
	Pathway Commons: MMAB
Context	iHOP: MMAB
	ligand binding site mutation search in PubMed: MMAB
	UCL Cancer Institute: MMAB
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 MMAB

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

LBS	AAchange of nsSNV	Cancer type	# samples
R190	R190H	COAD	2
R190	V188L	STAD	1
G87	G87E	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 MMAB

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
G87	G87E	0.006973242
R190	V188L	-0.90902881
R190	R190H	-0.85230392

(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 MMAB from PDB

PDB ID	PDB title	PDB structure
2IDX	Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP.

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Differential gene expression and gene-gene network for MMAB

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1855102	Methylmalonic aciduria cblB type	4	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID	AA change	Clinical significance	Origin	Phenotype IDs
200228	R190H	Pathogenic	Germline	GeneReviews:NBK1231 MedGen:C1855102 OMIM:251110 Orphanet:ORPHA28 Orphanet:ORPHA79311 MedGen:CN221809

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Pharmacological information for MMAB

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Approved	DB00200	Hydroxocobalamin	Small molecule

Gene-centered ligand-gene interaction network

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

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
ATP		ATP	2idx	C	G87
ATP		ATP	2idx	A	R190
ATP		ATP	2idx	C	R190

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Conservation information for LBS of MMAB

Multiple alignments for Q96EY8 in multiple species

LBS	AA sequence	# species	Species
E193	VCRRAERRVVP	3	Homo sapiens, Mus musculus, Bos taurus
F83	KDDQVFEAVGT	3	Homo sapiens, Mus musculus, Bos taurus
G63	IYTKTGDKGFS	3	Homo sapiens, Mus musculus, Bos taurus
G87	VFEAVGTTDEL	3	Homo sapiens, Mus musculus, Bos taurus
K61	PKIYTKTGDKG	3	Homo sapiens, Mus musculus, Bos taurus
K78	GERRPKDDQVF	2	Homo sapiens, Mus musculus
K78	GERRSKDDQVF	1	Bos taurus
N214	VAKFLNRLSDY	2	Homo sapiens, Mus musculus
N214	VVKFLNRLSDY	1	Bos taurus
R190	CRAVCRRAERR	3	Homo sapiens, Mus musculus, Bos taurus
R194	CRRAERRVVPL	3	Homo sapiens, Mus musculus, Bos taurus
S68	GDKGFSSTFTG	3	Homo sapiens, Mus musculus, Bos taurus
S69	DKGFSSTFTGE	3	Homo sapiens, Mus musculus, Bos taurus
T60	IPKIYTKTGDK	2	Homo sapiens, Mus musculus
T60	VPKIYTKTGDK	1	Bos taurus
T62	KIYTKTGDKGF	3	Homo sapiens, Mus musculus, Bos taurus