ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MSH2

Gene summary

Gene information	Gene symbol	MSH2
	Gene ID	4436
	Gene name	mutS homolog 2
	Synonyms	COCA1\|FCC1\|HNPCC\|HNPCC1\|LCFS2
	Cytomap	2p21-p16.3
	Type of gene	protein-coding
	Description	DNA mismatch repair protein Msh2hMSH2mutS homolog 2, colon cancer, nonpolyposis type 1
	Modification date	20180523
	UniProtAcc	P43246
	Context	PubMed: MSH2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
MSH2	GO:0006281	DNA repair	8942985
MSH2	GO:0006298	mismatch repair	7923193\|11555625
MSH2	GO:0006301	postreplication repair	7923193
MSH2	GO:0045910	negative regulation of DNA recombination	17715146
MSH2	GO:0051096	positive regulation of helicase activity	17715146

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Exon skipping events across known transcript of Ensembl for MSH2 from UCSC genome browser

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Gene isoform structures and expression levels for MSH2

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for MSH2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_325446	2	47635539:47635694:47637232:47637511:47639552:47639699	47637232:47637511	ENSG00000095002.8	ENST00000406134.1,ENST00000543555.1,ENST00000233146.2
exon_skip_325447	2	47637232:47637511:47639552:47639699:47641407:47641557	47639552:47639699	ENSG00000095002.8	ENST00000406134.1,ENST00000543555.1,ENST00000233146.2
exon_skip_325448	2	47639552:47639699:47641407:47641557:47643434:47643568	47641407:47641557	ENSG00000095002.8	ENST00000406134.1,ENST00000543555.1,ENST00000233146.2
exon_skip_325450	2	47690169:47690293:47693796:47693947:47698103:47698201	47693796:47693947	ENSG00000095002.8	ENST00000406134.1,ENST00000543555.1,ENST00000233146.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MSH2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_325446	2	47635539:47635694:47637232:47637511:47639552:47639699	47637232:47637511	ENSG00000095002.8	ENST00000233146.2,ENST00000543555.1,ENST00000406134.1
exon_skip_325448	2	47639552:47639699:47641407:47641557:47643434:47643568	47641407:47641557	ENSG00000095002.8	ENST00000233146.2,ENST00000543555.1,ENST00000406134.1
exon_skip_325450	2	47690169:47690293:47693796:47693947:47698103:47698201	47693796:47693947	ENSG00000095002.8	ENST00000233146.2,ENST00000543555.1,ENST00000406134.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for MSH2

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000233146	47693796	47693947	Frame-shift
ENST00000233146	47637232	47637511	In-frame
ENST00000233146	47639552	47639699	In-frame
ENST00000233146	47641407	47641557	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000233146	47693796	47693947	Frame-shift
ENST00000233146	47637232	47637511	In-frame
ENST00000233146	47641407	47641557	In-frame

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Infer the effects of exon skipping event on protein functional features for MSH2

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000233146	3324	934	47637232	47637511	590	868	122	215
ENST00000233146	3324	934	47639552	47639699	869	1015	215	264
ENST00000233146	3324	934	47641407	47641557	1016	1165	264	314

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000233146	3324	934	47637232	47637511	590	868	122	215
ENST00000233146	3324	934	47641407	47641557	1016	1165	264	314

Lost protein functional features of individual exon skipping events in TCGA.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P43246	122	215	117	124	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	147	152	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	155	158	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	160	167	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	172	179	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	197	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	2	934	Chain	ID=PRO_0000115183;Note=DNA mismatch repair protein Msh2
P43246	122	215	129	131	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2O8B
P43246	122	215	132	135	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	185	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	208	220	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	127	127	Natural variant	ID=VAR_019234;Note=In HNPCC1%3B presumed to enhance cancer risk considerably when associated with P-328%3B shows significantly decreased repair efficiency when associated with variant P-328. N->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:00002
P43246	122	215	139	139	Natural variant	ID=VAR_004472;Note=In HNPCC1. N->S
P43246	122	215	145	145	Natural variant	ID=VAR_004473;Note=In HNPCC1%3B unknown pathological significance%3B normal mismatch repair activity. I->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16451135,ECO:0000269\|PubMed:21120944,ECO:0000269\|PubMed:22581703;Dbxre
P43246	122	215	161	161	Natural variant	ID=VAR_012936;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. V->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11726306,ECO:0000269\|PubMed:17101
P43246	122	215	162	162	Natural variant	ID=VAR_054512;Note=In HNPCC1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17128465;Dbxref=dbSNP:rs63750773,PMID:17128465
P43246	122	215	162	162	Natural variant	ID=VAR_043747;Note=In HNPCC1%3B decreased mismatch repair activity%3B associated with an abnormal subcellular localization pattern%3B affects protein stability%3B loss of protein expression. G->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:00002
P43246	122	215	163	163	Natural variant	ID=VAR_043748;Note=In HNPCC1. V->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12200596;Dbxref=dbSNP:rs63750214,PMID:12200596
P43246	122	215	163	163	Natural variant	ID=VAR_022670;Note=In HNPCC1. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14635101;Dbxref=dbSNP:rs63750214,PMID:14635101
P43246	122	215	164	164	Natural variant	ID=VAR_043749;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. G->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	165	165	Natural variant	ID=VAR_067284;Note=In HNPCC1%3B unknown pathological significance%3B decreased mismatch repair activity. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22102614;Dbxref=dbSNP:rs587779163,PMID:22102614
P43246	122	215	167	167	Natural variant	ID=VAR_004474;Note=In HNPCC1%3B shows reduced mismatch binding%3B does not show a decreased expression level of the MutS alpha complex%3B not associated with an abnormal subcellular localization pattern%3B normal mismatch repair activity. D->H;Ontology_te
P43246	122	215	169	169	Natural variant	ID=VAR_043750;Note=In HNPCC1 and CRC%3B unknown pathological significance. I->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12792735,ECO:0000269\|PubMed:15996210;Dbxref=dbSNP:rs63750716,PMID:12792735,PMID:15996210
P43246	122	215	173	173	Natural variant	ID=VAR_043751;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	175	175	Natural variant	ID=VAR_043752;Note=In HNPCC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12655568;Dbxref=dbSNP:rs63751291,PMID:12655568
P43246	122	215	177	177	Natural variant	ID=VAR_067285;Note=In HNPCC1%3B requires 2 nucleotide substitutions%3B unknown pathological significance%3B normal mismatch repair activity. E->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22102614;Dbxref=PMID:22102614
P43246	122	215	187	187	Natural variant	ID=VAR_043753;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	187	187	Natural variant	ID=VAR_076352;Note=In HNPCC1%3B decreased mismatch repair activity%3B loss of protein expression. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21120944;Dbxref=dbSNP:rs63751444,PMID:21120944
P43246	122	215	198	198	Natural variant	ID=VAR_054513;Note=In HNPCC1. E->G;Dbxref=dbSNP:rs63750327
P43246	122	215	199	199	Natural variant	ID=VAR_012937;Note=In glioma%3B also associated with HNPCC1%3B no effect on MSH2 splicing. C->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18561205,ECO:0000269\|PubMed:9777949;Dbxref=dbSNP:rs63751110,PMID:18561205,PMID:9777949
P43246	122	215	203	203	Natural variant	ID=VAR_043754;Note=In CRC%3B unknown pathological significance%3B somatic mutation. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12792735;Dbxref=dbSNP:rs587779973,PMID:12792735
P43246	122	215	205	205	Natural variant	ID=VAR_068705;Note=Shows no defects%3B normal mismatch repair activity. E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22581703;Dbxref=dbSNP:rs63749984,PMID:22581703
P43246	122	215	168	171	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	223	227	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	2	934	Chain	ID=PRO_0000115183;Note=DNA mismatch repair protein Msh2
P43246	215	264	208	220	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	229	232	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	237	244	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	255	257	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	259	262	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	264	277	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	215	264	216	216	Natural variant	ID=VAR_012938;Note=In HNPCC1%3B unknown pathological significance%3B shows slightly reduced mismatch binding or release efficiency. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11726306;Dbxref=dbSNP:rs63749936,PMID:11726306
P43246	215	264	246	246	Natural variant	ID=VAR_043755;Note=In HNPCC1%3B unknown pathological significance. K->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:10573010;Dbxref=dbSNP:rs63750881,PMID:10573010
P43246	215	264	252	254	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2O8E
P43246	264	314	289	293	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	2	934	Chain	ID=PRO_0000115183;Note=DNA mismatch repair protein Msh2
P43246	264	314	264	277	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	279	281	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	283	285	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	304	309	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	265	314	Natural variant	ID=VAR_004475;Note=In HNPCC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9718327;Dbxref=PMID:9718327
P43246	264	314	272	272	Natural variant	ID=VAR_043756;Note=In HNPCC1%3B unknown pathological significance%3B shows slightly reduced mismatch binding or release efficiency%3B results in partial MSH2 exon 5 skipping%3B normal mismatch repair activity. A->V;Ontology_term=ECO:0000269,ECO:0000269,EC
P43246	264	314	283	283	Natural variant	ID=VAR_043757;Note=In HNPCC1. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15870828;Dbxref=dbSNP:rs63750381,PMID:15870828
P43246	264	314	305	305	Natural variant	ID=VAR_004476;Note=In HNPCC1%3B normal mismatch repair activity. A->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22102614,ECO:0000269\|PubMed:9311737;Dbxref=dbSNP:rs63751454,PMID:22102614,PMID:9311737

Lost protein functional features of individual exon skipping events in GTEx.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P43246	122	215	117	124	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	147	152	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	155	158	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	160	167	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	172	179	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	197	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	2	934	Chain	ID=PRO_0000115183;Note=DNA mismatch repair protein Msh2
P43246	122	215	129	131	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2O8B
P43246	122	215	132	135	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	185	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	208	220	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	122	215	127	127	Natural variant	ID=VAR_019234;Note=In HNPCC1%3B presumed to enhance cancer risk considerably when associated with P-328%3B shows significantly decreased repair efficiency when associated with variant P-328. N->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:00002
P43246	122	215	139	139	Natural variant	ID=VAR_004472;Note=In HNPCC1. N->S
P43246	122	215	145	145	Natural variant	ID=VAR_004473;Note=In HNPCC1%3B unknown pathological significance%3B normal mismatch repair activity. I->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16451135,ECO:0000269\|PubMed:21120944,ECO:0000269\|PubMed:22581703;Dbxre
P43246	122	215	161	161	Natural variant	ID=VAR_012936;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. V->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11726306,ECO:0000269\|PubMed:17101
P43246	122	215	162	162	Natural variant	ID=VAR_054512;Note=In HNPCC1. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17128465;Dbxref=dbSNP:rs63750773,PMID:17128465
P43246	122	215	162	162	Natural variant	ID=VAR_043747;Note=In HNPCC1%3B decreased mismatch repair activity%3B associated with an abnormal subcellular localization pattern%3B affects protein stability%3B loss of protein expression. G->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:00002
P43246	122	215	163	163	Natural variant	ID=VAR_043748;Note=In HNPCC1. V->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12200596;Dbxref=dbSNP:rs63750214,PMID:12200596
P43246	122	215	163	163	Natural variant	ID=VAR_022670;Note=In HNPCC1. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14635101;Dbxref=dbSNP:rs63750214,PMID:14635101
P43246	122	215	164	164	Natural variant	ID=VAR_043749;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. G->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	165	165	Natural variant	ID=VAR_067284;Note=In HNPCC1%3B unknown pathological significance%3B decreased mismatch repair activity. Y->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22102614;Dbxref=dbSNP:rs587779163,PMID:22102614
P43246	122	215	167	167	Natural variant	ID=VAR_004474;Note=In HNPCC1%3B shows reduced mismatch binding%3B does not show a decreased expression level of the MutS alpha complex%3B not associated with an abnormal subcellular localization pattern%3B normal mismatch repair activity. D->H;Ontology_te
P43246	122	215	169	169	Natural variant	ID=VAR_043750;Note=In HNPCC1 and CRC%3B unknown pathological significance. I->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12792735,ECO:0000269\|PubMed:15996210;Dbxref=dbSNP:rs63750716,PMID:12792735,PMID:15996210
P43246	122	215	173	173	Natural variant	ID=VAR_043751;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	175	175	Natural variant	ID=VAR_043752;Note=In HNPCC1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12655568;Dbxref=dbSNP:rs63751291,PMID:12655568
P43246	122	215	177	177	Natural variant	ID=VAR_067285;Note=In HNPCC1%3B requires 2 nucleotide substitutions%3B unknown pathological significance%3B normal mismatch repair activity. E->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22102614;Dbxref=PMID:22102614
P43246	122	215	187	187	Natural variant	ID=VAR_043753;Note=In HNPCC1%3B decreased mismatch repair activity%3B affects protein stability%3B loss of protein expression. L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17101317,ECO:0000269\|PubMed:18951462,ECO:0000
P43246	122	215	187	187	Natural variant	ID=VAR_076352;Note=In HNPCC1%3B decreased mismatch repair activity%3B loss of protein expression. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21120944;Dbxref=dbSNP:rs63751444,PMID:21120944
P43246	122	215	198	198	Natural variant	ID=VAR_054513;Note=In HNPCC1. E->G;Dbxref=dbSNP:rs63750327
P43246	122	215	199	199	Natural variant	ID=VAR_012937;Note=In glioma%3B also associated with HNPCC1%3B no effect on MSH2 splicing. C->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18561205,ECO:0000269\|PubMed:9777949;Dbxref=dbSNP:rs63751110,PMID:18561205,PMID:9777949
P43246	122	215	203	203	Natural variant	ID=VAR_043754;Note=In CRC%3B unknown pathological significance%3B somatic mutation. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12792735;Dbxref=dbSNP:rs587779973,PMID:12792735
P43246	122	215	205	205	Natural variant	ID=VAR_068705;Note=Shows no defects%3B normal mismatch repair activity. E->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:22581703;Dbxref=dbSNP:rs63749984,PMID:22581703
P43246	122	215	168	171	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	289	293	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	2	934	Chain	ID=PRO_0000115183;Note=DNA mismatch repair protein Msh2
P43246	264	314	264	277	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	279	281	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	283	285	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	296	298	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	304	309	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3THX
P43246	264	314	265	314	Natural variant	ID=VAR_004475;Note=In HNPCC1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9718327;Dbxref=PMID:9718327
P43246	264	314	272	272	Natural variant	ID=VAR_043756;Note=In HNPCC1%3B unknown pathological significance%3B shows slightly reduced mismatch binding or release efficiency%3B results in partial MSH2 exon 5 skipping%3B normal mismatch repair activity. A->V;Ontology_term=ECO:0000269,ECO:0000269,EC
P43246	264	314	283	283	Natural variant	ID=VAR_043757;Note=In HNPCC1. D->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15870828;Dbxref=dbSNP:rs63750381,PMID:15870828
P43246	264	314	305	305	Natural variant	ID=VAR_004476;Note=In HNPCC1%3B normal mismatch repair activity. A->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22102614,ECO:0000269\|PubMed:9311737;Dbxref=dbSNP:rs63751454,PMID:22102614,PMID:9311737

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SNVs in the skipped exons for MSH2

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

MSH2_STAD_exon_skip_325448_psi_boxplot.png
boxplot

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
ESCA	TCGA-L5-A43E-01	exon_skip_325446	47637233	47637511	47637242	47637242	Frame_Shift_Del	G	-	p.G126fs
KIRP	TCGA-2Z-A9JD-01	exon_skip_325446	47637233	47637511	47637500	47637500	Frame_Shift_Del	A	-	p.G211fs
HNSC	TCGA-CN-5369-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
LIHC	TCGA-DD-A39Y-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
STAD	TCGA-BR-8360-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
STAD	TCGA-BR-8363-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
STAD	TCGA-CG-4306-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
THYM	TCGA-ZB-A966-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.A230fs
THYM	TCGA-ZB-A966-01	exon_skip_325447	47639553	47639699	47639588	47639588	Frame_Shift_Del	A	-	p.R227fs
LIHC	TCGA-DD-A3A0-01	exon_skip_325448	47641408	47641557	47641494	47641494	Frame_Shift_Del	T	-	p.T293fs
COAD	TCGA-CM-4746-01	exon_skip_325450	47693797	47693947	47693836	47693837	Frame_Shift_Del	CA	-	p.517_517del
LIHC	TCGA-DD-A39Y-01	exon_skip_325450	47693797	47693947	47693875	47693875	Frame_Shift_Del	A	-	p.E530fs
READ	TCGA-EI-6882-01	exon_skip_325450	47693797	47693947	47693884	47693884	Frame_Shift_Del	T	-	p.L533fs
UCEC	TCGA-B5-A11N-01	exon_skip_325450	47693797	47693947	47693887	47693887	Frame_Shift_Del	G	-	p.R534fs
LIHC	TCGA-DD-A3A0-01	exon_skip_325450	47693797	47693947	47693895	47693895	Frame_Shift_Del	A	-	p.K537fs
KIRP	TCGA-G7-A8LB-01	exon_skip_325450	47693797	47693947	47693891	47693892	Frame_Shift_Ins	-	A	p.N535fs
PRAD	TCGA-EJ-7782-01	exon_skip_325450	47693797	47693947	47693894	47693895	Frame_Shift_Ins	-	A	p.K537fs
PRAD	TCGA-EJ-7782-01	exon_skip_325450	47693797	47693947	47693894	47693895	Frame_Shift_Ins	-	A	p.KK536fs
PRAD	TCGA-EJ-7782-01	exon_skip_325450	47693797	47693947	47693894	47693895	Frame_Shift_Ins	-	A	p.N536fs
UCEC	TCGA-D1-A174-01	exon_skip_325450	47693797	47693947	47693894	47693895	Frame_Shift_Ins	-	A	p.N536fs
LUAD	TCGA-17-Z053-01	exon_skip_325446	47637233	47637511	47637443	47637443	Nonsense_Mutation	C	T	p.Q193*
LUAD	TCGA-86-8585-01	exon_skip_325446	47637233	47637511	47637473	47637473	Nonsense_Mutation	G	T	p.G203*
MESO	TCGA-UD-AAC1-01	exon_skip_325446	47637233	47637511	47637509	47637509	Nonsense_Mutation	C	T	p.Q215*
BLCA	TCGA-E7-A7XN-01	exon_skip_325447	47639553	47639699	47639622	47639622	Nonsense_Mutation	C	T	p.Q239*
BLCA	TCGA-DK-A6AW-01	exon_skip_325448	47641408	47641557	47641447	47641447	Nonsense_Mutation	G	T	p.E278*
LIHC	TCGA-DD-A1EG-01	exon_skip_325447	47639553	47639699	47639551	47639551	Splice_Site	A	T	.
STAD	TCGA-BR-8487-01	exon_skip_325448	47641408	47641557	47641558	47641558	Splice_Site	G	T	.
PAAD	TCGA-IB-7651-01	exon_skip_325450	47693797	47693947	47693796	47693796	Splice_Site	G	T	.

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-BR-8487-01
	Cancer type: STAD
	ESID: exon_skip_325448
	Skipped exon start: 47641408
	Skipped exon end: 47641557
	Mutation start: 47641558
	Mutation end: 47641558
	Mutation type: Splice_Site
	Reference seq: G
	Mutation seq: T
	AAchange: .
exon_skip_110606_STAD_TCGA-BR-8487-01.png
exon_skip_13071_STAD_TCGA-BR-8487-01.png
exon_skip_311841_STAD_TCGA-BR-8487-01.png
exon_skip_313312_STAD_TCGA-BR-8487-01.png
exon_skip_313316_STAD_TCGA-BR-8487-01.png
exon_skip_313367_STAD_TCGA-BR-8487-01.png
exon_skip_325448_STAD_TCGA-BR-8487-01.png
exon_skip_33313_STAD_TCGA-BR-8487-01.png
exon_skip_359494_STAD_TCGA-BR-8487-01.png
exon_skip_430601_STAD_TCGA-BR-8487-01.png
exon_skip_430604_STAD_TCGA-BR-8487-01.png
exon_skip_430616_STAD_TCGA-BR-8487-01.png
exon_skip_440411_STAD_TCGA-BR-8487-01.png
exon_skip_440412_STAD_TCGA-BR-8487-01.png
exon_skip_458582_STAD_TCGA-BR-8487-01.png
exon_skip_468869_STAD_TCGA-BR-8487-01.png
exon_skip_475355_STAD_TCGA-BR-8487-01.png
exon_skip_495683_STAD_TCGA-BR-8487-01.png
exon_skip_503611_STAD_TCGA-BR-8487-01.png
exon_skip_56463_STAD_TCGA-BR-8487-01.png
exon_skip_68768_STAD_TCGA-BR-8487-01.png
exon_skip_84502_STAD_TCGA-BR-8487-01.png

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
OC316_OVARY	47637233	47637511	47637434	47637436	In_Frame_Del	CTC	-	p.L191del
OC314_OVARY	47637233	47637511	47637434	47637436	In_Frame_Del	CTC	-	p.L191del
KMH2_THYROID	47637233	47637511	47637237	47637237	Missense_Mutation	C	T	p.S124F
CCK81_LARGE_INTESTINE	47637233	47637511	47637390	47637390	Missense_Mutation	T	C	p.L175P
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47639553	47639699	47639569	47639569	Missense_Mutation	G	T	p.G221V
CL40_LARGE_INTESTINE	47639553	47639699	47639635	47639635	Missense_Mutation	G	A	p.R243Q
LB771HNC_UPPER_AERODIGESTIVE_TRACT	47639553	47639699	47639653	47639653	Missense_Mutation	A	C	p.K249T
LB771PBL_MATCHED_NORMAL_TISSUE	47639553	47639699	47639653	47639653	Missense_Mutation	A	C	p.K249T
KM12_LARGE_INTESTINE	47641408	47641557	47641538	47641538	Missense_Mutation	G	A	p.R308K
OC316_OVARY	47693797	47693947	47693857	47693857	Missense_Mutation	G	C	p.R524P
RL952_ENDOMETRIUM	47693797	47693947	47693857	47693857	Missense_Mutation	G	C	p.R524P
OC314_OVARY	47693797	47693947	47693857	47693857	Missense_Mutation	G	C	p.R524P
RL952_ENDOMETRIUM	47637233	47637511	47637509	47637509	Nonsense_Mutation	C	T	p.Q215*
SNU407_LARGE_INTESTINE	47641408	47641557	47641457	47641457	Nonsense_Mutation	C	G	p.S281*
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47693797	47693947	47693947	47693947	Splice_Site	G	A	p.S554N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MSH2

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MSH2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MSH2

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RelatedDrugs for MSH2

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for MSH2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
MSH2	C2936783	Colorectal cancer, hereditary nonpolyposis, type 1	48	UNIPROT
MSH2	C0009405	Hereditary Nonpolyposis Colorectal Neoplasms	4	CTD_human
MSH2	C0009404	Colorectal Neoplasms	1	CTD_human
MSH2	C0919267	ovarian neoplasm	1	CTD_human
MSH2	C2931459	Lynch syndrome I (site-specific colonic cancer)	1	CTD_human

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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