MSeqDR Central Portal

About
MSeqDR-LSDB
Tools
- Quick-Mitome for WES
- Quick-Mitome
- Quick-Mitome Report
- mtDNA Tool:
- mvTool
- Phy-Mer
- MToolBox
- mvTool for Haplogroup
- mvTool with HmtDB
- MitoMaster
- MitoTIP tRNA Scoring
- MSeq-OpenCGA
- Variant Tool:
- VariantOneStop
- HBCR Exome (Retired)
- POLG Patho. Server
- Data - Awsomics GeEx
- Expert Panel
- Panel Tool:
- Gene Panel Examiner
- Transgenomic_NuclearMitome
- Pedigree Maker
- json2table
Phenome-Disease
Collaboration
- Genesis (GEM.App)
- LeighMap
- Expert Panel
- Collaboration Zone
Submission
- Submit_Interpret_Variant
- Instructions

Hello! Guest! Please Login or Register! Clinician Mode

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 SMCHD1:

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
ENSG00000101596	SMCHD1	0	0	5	ENSG00000101596	ENST00000320876	ENSP00000326603	structural maintenance of chromosomes flexible hinge domain containing 1 [Source:HGNC Symbol;Acc:29090]	18	2655737	2805015	1	p11.32	2655737	2805015	SMCHD1	SMCHD1-001	HGNC Symbol	HGNC transcript name	14	36.8	protein_coding	protein_coding	ensembl_hava	ensembl_hava	KNOWN	KNOWN	23347	29090	SMCHD1	NM_015295	27512

MSeqDR Master Exome Data Set M1: 241 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	18	2655972	G	C	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	-	-	5'_UTR	NA	-	-	-	-	-	-	het	2
2	18	2655972	G	C	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	-	-	5'_UTR	NA	-	-	-	-	-	-	het	2
3	18	2656063	C	T	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	-	-	5'_UTR	NA	-	-	-	-	-	-	het	1
4	18	2656063	C	T	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	-	-	5'_UTR	NA	-	-	-	-	-	-	het	1
5	18	2656120	A	G	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.46A>G	p.T16A	non-syn	NA	-	-	-	-	-	-	het	1
6	18	2656120	A	G	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.46A>G	p.T16A	non-syn	NA	-	-	-	-	-	-	het	1
7	18	2656248	G	C	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.174G>C	p.A58A	syn	rs2430853	0.531	C=4539/G=3761;C=3344/G=612;C=7883/G=4373	-	-	-	-	hom	359
8	18	2656248	G	C	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.174G>C	p.A58A	syn	rs2430853	0.531	C=4539/G=3761;C=3344/G=612;C=7883/G=4373	-	-	-	-	het	475
9	18	2656248	G	C	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.174G>C	p.A58A	syn	rs2430853	0.531	C=4539/G=3761;C=3344/G=612;C=7883/G=4373	-	-	-	-	hom	359
10	18	2656248	G	C	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.174G>C	p.A58A	syn	rs2430853	0.531	C=4539/G=3761;C=3344/G=612;C=7883/G=4373	-	-	-	-	het	475
11	18	2666213	A	G	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.244A>G	p.I82V	non-syn	rs181045631	0.0029	-	lod=253:561	-	-	-	het	1
12	18	2666213	A	G	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.244A>G	p.I82V	non-syn	rs181045631	0.0029	-	lod=253:561	-	-	-	het	1
13	18	2666216	A	G	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.247A>G	p.T83A	non-syn	NA	-	-	lod=253:561	-	-	-	het	1
14	18	2666216	A	G	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.247A>G	p.T83A	non-syn	NA	-	-	lod=253:561	-	-	-	het	1
15	18	2666894	C	T	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.288C>T	p.T96T	syn	NA	-	T=1/C=8257;T=0/C=3816;T=1/C=12073	lod=125:485	-	-	-	het	1
16	18	2666894	C	T	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.288C>T	p.T96T	syn	NA	-	T=1/C=8257;T=0/C=3816;T=1/C=12073	lod=125:485	-	-	-	het	1
17	18	2667005	T	C	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	c.399T>C	p.Y133Y	syn	rs7239096	0.0694	C=7/T=8219;C=429/T=3325;C=436/T=11544	lod=642:660	-	-	-	het	5
18	18	2667005	T	C	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	c.399T>C	p.Y133Y	syn	rs7239096	0.0694	C=7/T=8219;C=429/T=3325;C=436/T=11544	lod=642:660	-	-	-	het	5
19	18	2667048	A	G	ENST00000261598	ENSG00000101596	2655737	2805015	ENSP00000261598	SMCHD1	1	SMHD1_HUMAN	-	-	+18bp 5'_splice_site	NA	-	-	-	-	-	-	het	2
20	18	2667048	A	G	ENST00000320876	ENSG00000101596	2655737	2805015	ENSP00000326603	SMCHD1	1	SMHD1_HUMAN	-	-	+18bp 5'_splice_site	NA	-	-	-	-	-	-	het	2

** 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.

As MSeqDR registered user , your accessible protected data set after login:

Select a dataset from the above drop-down list,
**click here to view variant details for this gene in selected data set**,
and click "Export" button to save as csv.

Transcripts and variants in the surrounding SMCHD1 18:2655737..2805015 region Gbrowse