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Examples Gene: MT-ND1, POLG, Region: M:1-1000 Variant: m.8993T>G, 1:g.10042757T>C rs3888511 MSCV_0000006, ClinVar: RCV000000015, Disease: Leigh syndrome, Phenotype: Retinopathy

MSeqDR Central Portal

MSeqDR Data Summary for the Term CLN3:

Ensembl Gene ID	Associated Gene Name	LSDB Genes	LSDB Variants	clinVar hits	Ensembl Gene ID	Ensembl Transcript ID	Ensembl Protein ID	Description	Chr	Gene Start	Gene End	Strand	Band	Transcript Start bp	Transcript End bp	Associated Gene Name	Associated Transcript Name	Associated Gene DB	Associated Transcript DB	Transcript count	pct GC content	Gene Biotype	Transcript Biotype	Source Gene	Source Transcript	Status gene	Status transcript	EntrezGene ID	HGNC ID	HGNC Symbol	RefSeq mRNA	Seq region id
ENSG00000261832	CLN3	1	0	121	ENSG00000261832	ENST00000568224	ENSP00000454253	Homo sapiens ceroid-lipofuscinosis, neuronal 3 (CLN3), transcript variant 5, mRNA. [Source:RefSeq mRNA;Acc:NM_001286109]	16	28477974	28503333	-1	p11.2	28477974	28503333	CLN3	CLN3-001	UniProtKB Gene Name	UniProt transcript name	1	49.1	protein_coding	nonsense_mediated_decay	havana	havana	NOVEL	KNOWN	1201	2074		NM_001286109	27514
ENSG00000188603	CLN3	1	0	121	ENSG00000188603	ENST00000566040		ceroid-lipofuscinosis, neuronal 3 [Source:HGNC Symbol;Acc:2074]	16	28477983	28506896	-1	p11.2	28503426	28506896	CLN3	CLN3-025	HGNC Symbol	HGNC transcript name	41	49.54	protein_coding	processed_transcript	ensembl_hava	havana	KNOWN	KNOWN	1201	2074	CLN3		27514

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MSeqDR Master Exome Data Set M1: 877 entries from same gene

No.	Chr	Position	Reference	Variant	EnsemblTranscriptID	EnsemblGeneID	Gene_Start	Gene_End	EnsemblProteinID	Gene	strand	Uniprot	cChange	pChange	Nature	dbSNP	Freq	EVS	phastCons	SIFT	Polyphen	HGMD	type	samples
1	16	28488782	G	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	-	-	+3bp 5'_splice_site	rs199979207	-	-	-	-	-	-	het	4
2	16	28488808	T	C	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	-	-	3'_UTR	NA	-	-	-	-	-	-	het	6
3	16	28488924	C	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.996G>A	p.A332A	syn	rs201206239	-	T=2/C=8598;T=0/C=4394;T=2/C=12992	-	-	-	-	het	1
4	16	28488941	G	A	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.979C>T	p.R327W	non-syn	rs139842473	-	A=1/G=8599;A=1/G=4393;A=2/G=12992	lod=109:471	DAMAGING	D	-	het	2
5	16	28488943	T	C	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.977A>G	p.H326R	non-syn	rs77595156	0.1869	C=272/T=8328;C=1180/T=3214;C=1452/T=11542	lod=109:471	TOLERATED	D	-	het	62
6	16	28488943	T	C	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.977A>G	p.H326R	non-syn	rs77595156	0.1869	C=272/T=8328;C=1180/T=3214;C=1452/T=11542	lod=109:471	TOLERATED	D	-	hom	8
7	16	28488944	G	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.976C>A	p.H326N	non-syn	rs146610181	0.0161	T=3/G=8597;T=103/G=4291;T=106/G=12888	lod=109:471	TOLERATED	D	-	het	2
8	16	28489045	G	A	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	-	-	+13bp 5'_splice_site	NA	-	A=0/G=8600;A=1/G=4393;A=1/G=12993	-	-	-	-	het	1
9	16	28489066	C	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.955G>A	p.A319T	non-syn	NA	-	-	lod=118:479	TOLERATED	P	-	het	1
10	16	28489072	T	C	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.949A>G	p.N317D	non-syn	NA	-	-	lod=118:479	DAMAGING	D	-	het	2
11	16	28493470	G	A	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.778C>T	p.R260C	non-syn	NA	-	-	lod=103:464	DAMAGING	B	-	het	1
12	16	28493535	G	C	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	-	-	-16bp 3'_splice_site	rs200023908	-	C=6/G=8592;C=1/G=4393;C=7/G=12985	-	-	-	-	het	3
13	16	28493821	C	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.649G>A	p.E217K	non-syn	rs121434286	-	-	lod=154:507	DAMAGING	D	HGMD	het	1
14	16	28493953	C	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.597G>A	p.V199V	syn	rs1142183	-	T=7/C=8593;T=0/C=4394;T=7/C=12987	lod=47:381	-	-	-	het	4
15	16	28495311	G	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	-	-	+16bp 5'_splice_site	rs200731769	-	-	-	-	-	-	het	1
16	16	28495346	C	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.537G>A	p.E179E	syn	rs73533466	0.0062	T=0/C=8600;T=47/C=4347;T=47/C=12947	-	-	-	-	hom	1
17	16	28495349	G	A	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.534C>T	p.T178T	syn	rs145967477	-	A=2/G=8598;A=6/G=4388;A=8/G=12986	-	-	-	-	het	1
18	16	28495363	G	A	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.520C>T	p.P174S	non-syn	NA	-	-	lod=33:343	DAMAGING	D	-	het	1
19	16	28495380	T	-CTG	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.500_502del	p.E168NA	non-syn	NA	-	-	-	-	-	-	het	1
20	16	28497696	G	T	ENST00000568224	ENSG00000261832	28477974	28503333	ENSP00000454253	CLN3	-1	-	c.415C>A	p.L139M	non-syn	rs150913606	-	T=2/G=8596;T=0/G=4392;T=2/G=12988	lod=83:441	DAMAGING	P	-	het	1

** A friendly reminder: guest user can access up to first 20 entries per gene from MSeqDR Master Exome Data Set M1. To gain access to the full power of MSeqDR, please login, or register, then request access to data.

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Select a dataset from the above drop-down list,
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Transcripts and variants in the surrounding CLN3 16:28477974..28503333 region Gbrowse