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 SND1

Gene summary

Basic gene Info.	Gene symbol	SND1
	Gene name	staphylococcal nuclease and tudor domain containing 1
	Synonyms	TDRD11\|p100
	Cytomap	UCSC genome browser: 7q31.3
	Type of gene	protein-coding
	RefGenes	NM_014390.2,
	Description	100 kDa coactivatorEBNA-2 co-activator (100kD)EBNA2 coactivator p100SND1-BRAF fusionTudor-SNp100 EBNA2 co-activatorp100 co-activatorstaphylococcal nuclease domain containing 1staphylococcal nuclease domain-containing protein 1tudor domain-contain
	Modification date	20141207
dbXrefs	MIM : 602181
	HGNC : HGNC
	Ensembl : ENSG00000197157
	HPRD : 03714
	Vega : OTTHUMG00000157560
Protein	UniProt: Q7KZF4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SND1
	BioGPS: 27044
Pathway	NCI Pathway Interaction Database: SND1
	KEGG: SND1
	REACTOME: SND1
	Pathway Commons: SND1
Context	iHOP: SND1
	ligand binding site mutation search in PubMed: SND1
	UCL Cancer Institute: SND1
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
GO:0001649	osteoblast differentiation	16210410

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Ligand binding site mutations for SND1

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
G41,P39	R40C	BRCA	1
Q699	V698M	COAD	1
K88	K88N	COAD	1
F250	K249N	COAD	1
E291	E291Q	LUAD	1
R423	P424S	SKCM	1
C440	C440F	SKCM	1
S254	S254L	SKCM	1
E689	E689K	STAD	1
G41,P39	R40L	STAD	1
I463	Y465C	UCEC	1
Y746	R747H	UCEC	1
Q825,N823	T824I	UCEC	1
F244,A246	A245S	UCEC	1
R327	R327S	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 SND1

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
S254	S254L	0.36457556
I463	Y465C	-1.1823474
R327	R327S	-1.1335731
F250	K249N	-1.1231541
E689	E689K	-0.97753914
Y746	R747H	-0.96474027
K88	K88N	-0.89091404
E291	E291Q	-0.80777964
Q699	V698M	-0.78025517
C440	C440F	-0.77981937
R423	P424S	-0.74562842
F244	A245S	-0.74154452
A246	A245S	-0.74154452
G41	R40C	-0.51548154
P39	R40C	-0.51548154
G41	R40L	-0.11767393
P39	R40L	-0.11767393
Q825	T824I	-0.080407203
N823	T824I	-0.080407203

(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 SND1 from PDB

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Differential gene expression and gene-gene network for SND1

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 SND1 and the right PPI network was created from samples without mutations in the LBS of SND1. 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 SND1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0004352	Autistic Disorder	1	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for SND1

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.

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SND1 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (GLY,ARG,ALA,ARG,ALA,ARG,ALA)	3omc	A	E689 Q699 Y746 N823
III		Peptide ligand (GLY,ARG,ALA,ARG,GLY,GLN)	3omg	A	E689 Y746 N823 Q825
III		Peptide ligand (ASN,SER,ASP,TRP,ASN,ALA,PRO,ALA,GLU,GLU,TRP,GLY,ASN,TRP,VAL)	4qmg	D	G41 K88 F244 A246 F250 S254
III		Peptide ligand (SER,ASP,TRP,ASN,ALA,PRO,ALA,GLU,GLU,TRP,GLY,ASN,TRP)	4qmg	A	P39 G41 K88 F244 A246 F250 S254
III		Peptide ligand (SER,ASP,TRP,ASN,ALA,PRO,ALA,GLU,GLU,TRP,GLY,ASN,TRP)	4qmg	E	P39 G41 K88 F244 A246 F250 S254 E291 R327
III		Peptide ligand (PRO,ASN,SER,ASP,TRP,ASN,ALA,PRO,ALA,GLU,GLU,TRP,GLY,ASN,TRP)	4qmg	B	P39 K88 F244 A246 F250 S254 E291 R327
III		Peptide ligand (ALA,ASP,PRO,ASN,SER,ASP,TRP,ASN,ALA,PRO,ALA,GLU,GLU,TRP,GLY,ASN,TRP)	4qmg	C	P39 K88 F244 F250 S254 E291
ARG		ARGININE	3omc	B	Y746 N823
III		Peptide ligand (ARG,ALA,ARG,GLY,GLN)	3omg	B	Y746 N823 Q825

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Conservation information for LBS of SND1

Multiple alignments for Q7KZF4 in multiple species

LBS	AA sequence	# species	Species
A246	PEPFAAEAKFF	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
A246	QEPCGDEAKQF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C440	FSERTCATVTI	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
C440	INN--CTVKLS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D260	RLLQRDVQI-I	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D260	RLLQRNVVIEL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D742	IAKFVDGEWYR	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D742	AISALDNAMYR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E247	EPFAAEAKFFT	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E247	EPCGDEAKQFV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E291	ELLLKEGFARC	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E291	TFLLSSGLGRV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E689	----TEITDDL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E689	DIVLSDIAEDG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E708	G-TQLEKLMEN	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E708	GIQQLETLMSD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F244	ETPEPFAAEAK	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F244	SEQEPCGDEAK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F250	AAEAKFFTESR	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F250	GDEAKQFVVTR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F251	AEAKFFTESRL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F251	DEAKQFVVTRL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F293	LLKEGFARCVD	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F293	LLSSGLGRVAD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F535	VVEYVFSGSRL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F535	IIENVISGSRF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F686	SYKPVFV----	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F686	VKEPIYLDIVL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F740	FCIAKFVDGEW	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F740	-AAISALDNAM	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G41	RGQPRGGPPPE	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G41	LIKDNAKKITE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G42	GQPRGGPPPER	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G42	IKDNAKKITEK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G563	IECPRGARNLP	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G563	IRTPRTARNDQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G704	QDVETG-TQLE	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G704	QIIGTGIQQLE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G92	RKKLIGKEVCF	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G92	RRLVVGRPASV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H279	LGTILHPNGNI	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H279	LGNVLHPAGNI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H475	DQRSSHYDELL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H475	VDRSPIYDFLI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I463	GLATVIRYRQD	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I463	GYATVIRYRMD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I91	LRKKLIGKEVC	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I91	SRRLVVGRPAS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K88	REFLRKKLIGK	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K88	QEFSRRLVVGR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K93	KKLIGKEVCFT	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K93	RLVVGRPASVS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L256	FTESRLLQRDV	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
L256	FVVTRLLQRNV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L287	GNITELLLKEG	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
L287	GNIATFLLSSG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N281	TILHPNGNITE	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N281	NVLHPAGNIAT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N416	IGKKVNVTVDY	3	Homo sapiens, Bos taurus, Mus musculus
N416	IGKRVQVSLDF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N416	IGKKVSVTVDY	1	Rattus norvegicus
N768	YIDYGNREILP	3	Bos taurus, Mus musculus, Rattus norvegicus
N768	YIDYGNREVLP	1	Homo sapiens
N768	LYDYGSVEQIP	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N823	VRDIQNTQCLL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N823	FRELAMNKGLV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P39	IVRGQPRGGPP	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P39	NILIKDNAKKI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P427	IRPASPATETV	3	Homo sapiens, Mus musculus, Rattus norvegicus
P427	IRPGQ---NDL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P427	IRPASPATDTV	1	Bos taurus
P43	QPRGGPPPERQ	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P43	KDNAKKITEKQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q258	ESRLLQRDVQI	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q258	VTRLLQRNVVI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q38	IIVRGQPRGGP	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q38	FNILIKDNAKK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q699	LHFYVQDVETG	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q699	GKFSFQIIGTG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q825	DIQNTQCLL-N	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q825	ELAMNKGLVAK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R255	FFTESRLLQRD	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R255	QFVVTRLLQRN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R259	SRLLQRDVQI-	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R259	TRLLQRNVVIE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R324	KERRLRIWRDY	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R324	KISRLGIWKNI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R327	RLRIWRDYVAP	2	Homo sapiens, Bos taurus
R327	RLRIWRDYVPP	2	Mus musculus, Rattus norvegicus
R327	RLGIWKNISVS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R374	HLSSIRPPRLE	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R374	QLSSIRHPRPS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R377	SIRPPRLEGEN	2	Homo sapiens, Bos taurus
R377	SIRPPRLEGDN	2	Mus musculus, Rattus norvegicus
R377	SIRHPRPSNEK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R423	TVDYIRPASPA	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R423	SLDFIRPGQ--	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R539	VFSGSRLKLYL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R539	VISGSRFRCFC	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R562	GIECPRGARNL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R562	GIRTPRTARND	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R565	CPRGARNLPGL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R565	TPRTARNDQ--	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R87	AREFLRKKLIG	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R87	AQEFSRRLVVG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S254	KFFTESRLLQR	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S254	KQFVVTRLLQR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S426	YIRPASPATET	3	Homo sapiens, Mus musculus, Rattus norvegicus
S426	FIRPGQ---ND	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S426	YIRPASPATDT	1	Bos taurus
S536	VEYVFSGSRLK	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S536	IENVISGSRFR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T418	KKVNVTVDYIR	3	Homo sapiens, Bos taurus, Mus musculus
T418	KRVQVSLDFIR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T418	KKVSVTVDYIR	1	Rattus norvegicus
T444	TCATVTIGGIN	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T444	-CTVKLSDGTN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T688	V----TEITDD	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T688	LDIVLSDIAED	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T705	VETG-TQLEKL	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T705	IGTGIQQLETL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V701	FYVQDVETG-T	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V701	FSFQIIGTGIQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V741	CIAKFVDGEWY	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V741	AAISALDNAMY	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y421	NVTVDYIRPAS	3	Homo sapiens, Bos taurus, Mus musculus
Y421	QVSLDFIRPGQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y421	SVTVDYIRPAS	1	Rattus norvegicus
Y746	VDGEWYRARVE	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y746	LDNAMYRGRVL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y763	-VHVFYIDYGN	3	Bos taurus, Mus musculus, Rattus norvegicus
Y763	-IHVFYIDYGN	1	Homo sapiens
Y763	AADVLLYDYGS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y766	VFYIDYGNREI	3	Bos taurus, Mus musculus, Rattus norvegicus
Y766	VFYIDYGNREV	1	Homo sapiens
Y766	VLLYDYGSVEQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)