MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 7 transcript(s)...
Querying Taster for transcript #1: ENST00000405837
Querying Taster for transcript #2: ENST00000278893
Querying Taster for transcript #3: ENST00000360796
Querying Taster for transcript #4: ENST00000403550
Querying Taster for transcript #5: ENST00000407022
Querying Taster for transcript #6: ENST00000421906
Querying Taster for transcript #7: ENST00000433053
MT speed 0 s - this script 4.111313 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BSCL2	disease_causing_automatic	0.999961485513863	simple_aae			0	N152S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999961485513863	simple_aae			0	N152S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999961485513863	simple_aae			0	N152S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999971221038735	simple_aae			0	N88S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999971221038735	simple_aae			0	N88S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999971221038735	simple_aae			0	N88S	single base exchange	rs137852972		show file
BSCL2	disease_causing_automatic	0.999971221038735	simple_aae			0	N88S	single base exchange	rs137852972		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999961485513863 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000405837

Genbank transcript ID

N/A

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.455A>G
cDNA.952A>G
g.7347A>G

AA changes

N152S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

152

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs4543 (pathogenic for Spastic paraplegia 17|Distal hereditary motor neuronopathy type 5|Charcot-Marie-Tooth disease, type 2|not specified|NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE VC|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040381)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040381)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040381)

regulatory features

BATF, Transcription Factor, BATF Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

152

mutated

all conserved

152

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1395 / 1395

position (AA) of stopcodon in wt / mu AA sequence

465 / 465

position of stopcodon in wt / mu cDNA

1892 / 1892

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

498 / 498

chromosome

strand

-1

last intron/exon boundary

1738

theoretical NMD boundary in CDS

1190

length of CDS

1395

coding sequence (CDS) position

455

cDNA position
(for ins/del: last normal base / first normal base)

952

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ANVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGAG
PEGQEESTPQ SDVTEDGESP EDPSGTEGQL SEEEKPDQQP LSGEEELEPE ASDGSGSWED
AALLTEANLP APAPASASAP VLETLGSSEP AGGALRQRPT CSSS*

mutated AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ASVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGAG
PEGQEESTPQ SDVTEDGESP EDPSGTEGQL SEEEKPDQQP LSGEEELEPE ASDGSGSWED
AALLTEANLP APAPASASAP VLETLGSSEP AGGALRQRPT CSSS*

speed

0.38 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999961485513863 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000360796

Genbank transcript ID

NM_001122955

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.455A>G
cDNA.658A>G
g.7347A>G

AA changes

N152S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

152

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

152

mutated

all conserved

152

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1389 / 1389

position (AA) of stopcodon in wt / mu AA sequence

463 / 463

position of stopcodon in wt / mu cDNA

1592 / 1592

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

204 / 204

chromosome

strand

-1

last intron/exon boundary

1438

theoretical NMD boundary in CDS

1184

length of CDS

1389

coding sequence (CDS) position

455

cDNA position
(for ins/del: last normal base / first normal base)

658

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ANVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGPE
GQEESTPQSD VTEDGESPED PSGTEGQLSE EEKPDQQPLS GEEELEPEAS DGSGSWEDAA
LLTEANLPAP APASASAPVL ETLGSSEPAG GALRQRPTCS SS*

mutated AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ASVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGPE
GQEESTPQSD VTEDGESPED PSGTEGQLSE EEKPDQQPLS GEEELEPEAS DGSGSWEDAA
LLTEANLPAP APASASAPVL ETLGSSEPAG GALRQRPTCS SS*

speed

0.38 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999961485513863 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000433053

Genbank transcript ID

N/A

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.455A>G
cDNA.1012A>G
g.7347A>G

AA changes

N152S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

152

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

152

mutated

all conserved

152

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1389 / 1389

position (AA) of stopcodon in wt / mu AA sequence

463 / 463

position of stopcodon in wt / mu cDNA

1946 / 1946

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

558 / 558

chromosome

strand

-1

last intron/exon boundary

1792

theoretical NMD boundary in CDS

1184

length of CDS

1389

coding sequence (CDS) position

455

cDNA position
(for ins/del: last normal base / first normal base)

1012

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ANVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGPE
GQEESTPQSD VTEDGESPED PSGTEGQLSE EEKPDQQPLS GEEELEPEAS DGSGSWEDAA
LLTEANLPAP APASASAPVL ETLGSSEPAG GALRQRPTCS SS*

mutated AA sequence

MSTEKVDQKE EAGEKEVCGD QIKGPDKEEE PPAAASHGQG WRPGGRAARN ARPEPGARHP
ALPAMVNDPP VPALLWAQEV GQVLAGRARR LLLQFGVLFC TILLLLWVSV FLYGSFYYSY
MPTVSHLSPV HFYYRTDCDS STTSLCSFPV ASVSLTKGGR DRVLMYGQPY RVTLELELPE
SPVNQDLGMF LVTISCYTRG GRIISTSSRS VMLHYRSDLL QMLDTLVFSS LLLFGFAEQK
QLLEVELYAD YRENSYVPTT GAIIEIHSKR IQLYGAYLRI HAHFTGLRYL LYNFPMTCAF
IGVASNFTFL SVIVLFSYMQ WVWGGIWPRH RFSLQVNIRK RDNSRKEVQR RISAHQPGPE
GQEESTPQSD VTEDGESPED PSGTEGQLSE EEKPDQQPLS GEEELEPEAS DGSGSWEDAA
LLTEANLPAP APASASAPVL ETLGSSEPAG GALRQRPTCS SS*

speed

0.30 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999971221038735 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000278893

Genbank transcript ID

NM_001130702

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.263A>G
cDNA.481A>G
g.7347A>G

AA changes

N88S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost
88	88	CARBOHYD	N-linked (GlcNAc...).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

864 / 864

position (AA) of stopcodon in wt / mu AA sequence

288 / 288

position of stopcodon in wt / mu cDNA

1082 / 1082

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

219 / 219

chromosome

strand

-1

last intron/exon boundary

1119

theoretical NMD boundary in CDS

850

length of CDS

864

coding sequence (CDS) position

263

cDNA position
(for ins/del: last normal base / first normal base)

481

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRLTSEKE TIPGRKSNEG
SLLISQGLKA RRSQLRNQML QRMVRALKIP QGQRVSCPRR RNQISSP*

mutated AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVASVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRLTSEKE TIPGRKSNEG
SLLISQGLKA RRSQLRNQML QRMVRALKIP QGQRVSCPRR RNQISSP*

speed

0.36 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999971221038735 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000403550

Genbank transcript ID

N/A

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.263A>G
cDNA.687A>G
g.7347A>G

AA changes

N88S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost
88	88	CARBOHYD	N-linked (GlcNAc...).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1197 / 1197

position (AA) of stopcodon in wt / mu AA sequence

399 / 399

position of stopcodon in wt / mu cDNA

1621 / 1621

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

425 / 425

chromosome

strand

-1

last intron/exon boundary

1467

theoretical NMD boundary in CDS

992

length of CDS

1197

coding sequence (CDS) position

263

cDNA position
(for ins/del: last normal base / first normal base)

687

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

mutated AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVASVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

speed

0.89 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999971221038735 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000407022

Genbank transcript ID

NM_032667

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.263A>G
cDNA.510A>G
g.7347A>G

AA changes

N88S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost
88	88	CARBOHYD	N-linked (GlcNAc...).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1197 / 1197

position (AA) of stopcodon in wt / mu AA sequence

399 / 399

position of stopcodon in wt / mu cDNA

1444 / 1444

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

248 / 248

chromosome

strand

-1

last intron/exon boundary

1290

theoretical NMD boundary in CDS

992

length of CDS

1197

coding sequence (CDS) position

263

cDNA position
(for ins/del: last normal base / first normal base)

510

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

mutated AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVASVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

speed

0.88 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999971221038735 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040381)
known disease mutation: rs4543 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:62469971T>CN/A show variant in all transcripts IGV

HGNC symbol

BSCL2

Ensembl transcript ID

ENST00000421906

Genbank transcript ID

N/A

UniProt peptide

Q96G97

alteration type

single base exchange

alteration region

CDS

DNA changes

c.263A>G
cDNA.454A>G
g.7347A>G

AA changes

N88S Score: 46 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs137852972

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.532	1
	4.113	1
(flanking)	4.113	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	7343	wt: 0.9563 / mu: 0.9756 (marginal change - not scored)	wt: CACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAG mu: CACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAG	gttg\|CCAA
Acc marginally increased	7340	wt: 0.9418 / mu: 0.9656 (marginal change - not scored)	wt: CCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACT mu: CCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACT	cctg\|TTGC
Acc marginally increased	7339	wt: 0.9823 / mu: 0.9923 (marginal change - not scored)	wt: ACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGAC mu: ACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGAC	ccct\|GTTG
Acc marginally increased	7338	wt: 0.9229 / mu: 0.9398 (marginal change - not scored)	wt: CACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGA mu: CACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGA	tccc\|TGTT
Acc marginally increased	7346	wt: 0.9838 / mu: 0.9901 (marginal change - not scored)	wt: TCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGT mu: TCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGT	gcca\|ATGT
Acc marginally increased	7337	wt: 0.9416 / mu: 0.9448 (marginal change - not scored)	wt: CCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTG mu: CCACCTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTG	ttcc\|CTGT
Acc marginally increased	7341	wt: 0.8919 / mu: 0.9018 (marginal change - not scored)	wt: CTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTA mu: CTCACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTA	ctgt\|TGCC
Acc marginally increased	7344	wt: 0.6579 / mu: 0.6771 (marginal change - not scored)	wt: ACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGG mu: ACTCTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGG	ttgc\|CAAT
Acc marginally increased	7348	wt: 0.3058 / mu: 0.3070 (marginal change - not scored)	wt: TGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGG mu: TGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTGG	caat\|GTCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000003784

152

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000018428

Mmusculus

all identical

ENSMUSG00000071657

148

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000037008

123

Dmelanogaster

all conserved

FBgn0040336

110

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000006021

protein features

start (aa)	end (aa)	feature	details
48	242	TOPO_DOM	Lumenal (Potential).	lost
88	88	CARBOHYD	N-linked (GlcNAc...).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1197 / 1197

position (AA) of stopcodon in wt / mu AA sequence

399 / 399

position of stopcodon in wt / mu cDNA

1388 / 1388

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

192 / 192

chromosome

strand

-1

last intron/exon boundary

1234

theoretical NMD boundary in CDS

992

length of CDS

1197

coding sequence (CDS) position

263

cDNA position
(for ins/del: last normal base / first normal base)

454

gDNA position
(for ins/del: last normal base / first normal base)

7347

chromosomal position
(for ins/del: last normal base / first normal base)

62469971

original gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered gDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

original cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTG

altered cDNA sequence snippet

CTGCTCCTTCCCTGTTGCCAGTGTCTCGCTGACTAAGGGTG

wildtype AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVANVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

mutated AA sequence

MVNDPPVPAL LWAQEVGQVL AGRARRLLLQ FGVLFCTILL LLWVSVFLYG SFYYSYMPTV
SHLSPVHFYY RTDCDSSTTS LCSFPVASVS LTKGGRDRVL MYGQPYRVTL ELELPESPVN
QDLGMFLVTI SCYTRGGRII STSSRSVMLH YRSDLLQMLD TLVFSSLLLF GFAEQKQLLE
VELYADYREN SYVPTTGAII EIHSKRIQLY GAYLRIHAHF TGLRYLLYNF PMTCAFIGVA
SNFTFLSVIV LFSYMQWVWG GIWPRHRFSL QVNIRKRDNS RKEVQRRISA HQPGPEGQEE
STPQSDVTED GESPEDPSGT EGQLSEEEKP DQQPLSGEEE LEPEASDGSG SWEDAALLTE
ANLPAPAPAS ASAPVLETLG SSEPAGGALR QRPTCSSS*

speed

0.43 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems