MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000520933
Querying Taster for transcript #2: ENST00000240132
Querying Taster for transcript #3: ENST00000407991
MT speed 0 s - this script 4.710418 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNA2	disease_causing_automatic	0.999999967722752	simple_aae		affected	0	I264N	single base exchange	rs104894063		show file
CHRNA2	disease_causing_automatic	0.999999981668058	simple_aae		affected	0	I279N	single base exchange	rs104894063		show file
CHRNA2	disease_causing_automatic	0.999999981668058	simple_aae		affected	0	I279N	single base exchange	rs104894063		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999967722752 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062512)
known disease mutation: rs17504 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:27321124A>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNA2

Ensembl transcript ID

ENST00000240132

Genbank transcript ID

N/A

UniProt peptide

Q15822

alteration type

single base exchange

alteration region

CDS

DNA changes

c.791T>A
cDNA.1365T>A
g.16277T>A

AA changes

I264N Score: 194 explain score(s)

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

264

frameshift

known variant

Reference ID: rs104894063
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17504 (pathogenic for Epilepsy, nocturnal frontal lobe, type 4) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM062512)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062512)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062512)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.665	1
	4.391	1
(flanking)	4.391	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	16277	wt: 0.7866 / mu: 0.7949 (marginal change - not scored)	wt: CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG mu: CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG	tcat\|CTCC
Acc marginally increased	16271	wt: 0.8986 / mu: 0.9303 (marginal change - not scored)	wt: CAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTG mu: CAACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTG	gcct\|GCTC
Acc marginally increased	16280	wt: 0.7272 / mu: 0.7622 (marginal change - not scored)	wt: CATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGGTCT mu: CATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGGTCT	tctc\|CTGC
Acc increased	16272	wt: 0.34 / mu: 0.39	wt: AACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGT mu: AACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGT	cctg\|CTCA
Donor gained	16272	0.75	mu: TGCCTGCTCAACTCC	CCTG\|ctca

distance from splice site

387

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

264

mutated

not conserved

264

Ptroglodytes

all identical

ENSPTRG00000020105

279

Mmulatta

all identical

ENSMMUG00000021514

279

Fcatus

all identical

ENSFCAG00000014421

277

Mmusculus

all identical

ENSMUSG00000022041

256

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008002

257

Drerio

all identical

ENSDARG00000006602

257

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017553

237

protein features

start (aa)	end (aa)	feature	details
27	264	TOPO_DOM	Extracellular.	lost
265	289	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
297	315	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	352	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
353	502	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
503	521	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1545 / 1545

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

515 / 515

position of stopcodon in wt / mu cDNA

2119 / 2119

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

575 / 575

chromosome

strand

-1

last intron/exon boundary

1994

theoretical NMD boundary in CDS

1369

length of CDS

1545

coding sequence (CDS) position

791

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

1365

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

16277

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

27321124

original gDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered gDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

original cDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered cDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

wildtype AA sequence

MGPSCPVFLS FTKLSLWWLL LTPAGGEEAK RPPPRAPGDP LSSPSPTALP QGGSHTETED
RLFKHLFRGY NRWARPVPNT SDVDEKNQMM TTNVWLKQEW SDYKLRWNPT DFGNITSLRV
PSEMIWIPDI VLYNNADGEF AVTHMTKAHL FSTGTVHWVP PAIYKSSCSI DVTFFPFDQQ
NCKMKFGSWT YDKAKIDLEQ MEQTVDLKDY WESGEWAIVN ATGTYNSKKY DCCAEIYPDV
TYAFVIRRLP LFYTINLIIP CLLISCLTVL VFYLPSDCGE KITLCISVLL SLTVFLLLIT
EIIPSTSLVI PLIGEYLLFT MIFVTLSIVI TVFVLNVHHR SPSTHTMPHW VRGALLGCVP
RWLLMNRPPP PVELCHPLRL KLSPSYHWLE SNVDAEEREV VVEEEDRWAC AGHVAPSVGT
LCSHGHLHSG ASGPKAEALL QEGELLLSPH MQKALEGVHY IADHLRSEDA DSSVKEDWKY
VAMVIDRIFL WLFIIVCFLG TIGLFLPPFL AGMI*

mutated AA sequence

MGPSCPVFLS FTKLSLWWLL LTPAGGEEAK RPPPRAPGDP LSSPSPTALP QGGSHTETED
RLFKHLFRGY NRWARPVPNT SDVDEKNQMM TTNVWLKQEW SDYKLRWNPT DFGNITSLRV
PSEMIWIPDI VLYNNADGEF AVTHMTKAHL FSTGTVHWVP PAIYKSSCSI DVTFFPFDQQ
NCKMKFGSWT YDKAKIDLEQ MEQTVDLKDY WESGEWAIVN ATGTYNSKKY DCCAEIYPDV
TYAFVIRRLP LFYTINLIIP CLLNSCLTVL VFYLPSDCGE KITLCISVLL SLTVFLLLIT
EIIPSTSLVI PLIGEYLLFT MIFVTLSIVI TVFVLNVHHR SPSTHTMPHW VRGALLGCVP
RWLLMNRPPP PVELCHPLRL KLSPSYHWLE SNVDAEEREV VVEEEDRWAC AGHVAPSVGT
LCSHGHLHSG ASGPKAEALL QEGELLLSPH MQKALEGVHY IADHLRSEDA DSSVKEDWKY
VAMVIDRIFL WLFIIVCFLG TIGLFLPPFL AGMI*

speed

1.28 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: 0.999999981668058 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062512)
known disease mutation: rs17504 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:27321124A>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNA2

Ensembl transcript ID

ENST00000520933

Genbank transcript ID

N/A

UniProt peptide

Q15822

alteration type

single base exchange

alteration region

CDS

DNA changes

c.836T>A
cDNA.990T>A
g.16277T>A

AA changes

I279N Score: 194 explain score(s)

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

279

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.665	1
	4.391	1
(flanking)	4.391	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	16277	wt: 0.7866 / mu: 0.7949 (marginal change - not scored)	wt: CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG mu: CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG	tcat\|CTCC
Acc marginally increased	16271	wt: 0.8986 / mu: 0.9303 (marginal change - not scored)	wt: CAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTG mu: CAACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTG	gcct\|GCTC
Acc marginally increased	16280	wt: 0.7272 / mu: 0.7622 (marginal change - not scored)	wt: CATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGGTCT mu: CATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGGTCT	tctc\|CTGC
Acc increased	16272	wt: 0.34 / mu: 0.39	wt: AACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGT mu: AACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGT	cctg\|CTCA
Donor gained	16272	0.75	mu: TGCCTGCTCAACTCC	CCTG\|ctca

distance from splice site

387

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

279

mutated

not conserved

279

Ptroglodytes

all identical

ENSPTRG00000020105

279

Mmulatta

all identical

ENSMMUG00000021514

279

Fcatus

all identical

ENSFCAG00000014421

277

Mmusculus

all identical

ENSMUSG00000022041

256

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008002

257

Drerio

all identical

ENSDARG00000006602

257

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017553

237

protein features

start (aa)	end (aa)	feature	details
265	289	TRANSMEM	Helical; (Potential).	lost
297	315	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	352	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
353	502	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
503	521	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1590 / 1590

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

530 / 530

position of stopcodon in wt / mu cDNA

1744 / 1744

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

155 / 155

chromosome

strand

-1

last intron/exon boundary

1619

theoretical NMD boundary in CDS

1414

length of CDS

1590

coding sequence (CDS) position

836

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

990

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

16277

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

27321124

original gDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered gDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

original cDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered cDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

wildtype AA sequence

MGPSCPVFLS FTKLSLWWLL LTPAGGEEAK RPPPRAPGDP LSSPSPTALP QGGSHTETED
RLFKHLFRGY NRWARPVPNT SDVVIVRFGL SIAQLIDVDE KNQMMTTNVW LKQEWSDYKL
RWNPTDFGNI TSLRVPSEMI WIPDIVLYNN ADGEFAVTHM TKAHLFSTGT VHWVPPAIYK
SSCSIDVTFF PFDQQNCKMK FGSWTYDKAK IDLEQMEQTV DLKDYWESGE WAIVNATGTY
NSKKYDCCAE IYPDVTYAFV IRRLPLFYTI NLIIPCLLIS CLTVLVFYLP SDCGEKITLC
ISVLLSLTVF LLLITEIIPS TSLVIPLIGE YLLFTMIFVT LSIVITVFVL NVHHRSPSTH
TMPHWVRGAL LGCVPRWLLM NRPPPPVELC HPLRLKLSPS YHWLESNVDA EEREVVVEEE
DRWACAGHVA PSVGTLCSHG HLHSGASGPK AEALLQEGEL LLSPHMQKAL EGVHYIADHL
RSEDADSSVK EDWKYVAMVI DRIFLWLFII VCFLGTIGLF LPPFLAGMI*

mutated AA sequence

MGPSCPVFLS FTKLSLWWLL LTPAGGEEAK RPPPRAPGDP LSSPSPTALP QGGSHTETED
RLFKHLFRGY NRWARPVPNT SDVVIVRFGL SIAQLIDVDE KNQMMTTNVW LKQEWSDYKL
RWNPTDFGNI TSLRVPSEMI WIPDIVLYNN ADGEFAVTHM TKAHLFSTGT VHWVPPAIYK
SSCSIDVTFF PFDQQNCKMK FGSWTYDKAK IDLEQMEQTV DLKDYWESGE WAIVNATGTY
NSKKYDCCAE IYPDVTYAFV IRRLPLFYTI NLIIPCLLNS CLTVLVFYLP SDCGEKITLC
ISVLLSLTVF LLLITEIIPS TSLVIPLIGE YLLFTMIFVT LSIVITVFVL NVHHRSPSTH
TMPHWVRGAL LGCVPRWLLM NRPPPPVELC HPLRLKLSPS YHWLESNVDA EEREVVVEEE
DRWACAGHVA PSVGTLCSHG HLHSGASGPK AEALLQEGEL LLSPHMQKAL EGVHYIADHL
RSEDADSSVK EDWKYVAMVI DRIFLWLFII VCFLGTIGLF LPPFLAGMI*

speed

1.30 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999981668058 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062512)
known disease mutation: rs17504 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:27321124A>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNA2

Ensembl transcript ID

ENST00000407991

Genbank transcript ID

NM_000742

UniProt peptide

Q15822

alteration type

single base exchange

alteration region

CDS

DNA changes

c.836T>A
cDNA.1445T>A
g.16277T>A

AA changes

I279N Score: 194 explain score(s)

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

279

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.665	1
	4.391	1
(flanking)	4.391	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	16277	wt: 0.7866 / mu: 0.7949 (marginal change - not scored)	wt: CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG mu: CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG	tcat\|CTCC
Acc marginally increased	16271	wt: 0.8986 / mu: 0.9303 (marginal change - not scored)	wt: CAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTG mu: CAACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTG	gcct\|GCTC
Acc marginally increased	16280	wt: 0.7272 / mu: 0.7622 (marginal change - not scored)	wt: CATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGGTCT mu: CATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGGTCT	tctc\|CTGC
Acc increased	16272	wt: 0.34 / mu: 0.39	wt: AACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGT mu: AACCTCATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGT	cctg\|CTCA
Donor gained	16272	0.75	mu: TGCCTGCTCAACTCC	CCTG\|ctca

distance from splice site

387

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

279

mutated

not conserved

279

Ptroglodytes

all identical

ENSPTRG00000020105

279

Mmulatta

all identical

ENSMMUG00000021514

279

Fcatus

all identical

ENSFCAG00000014421

277

Mmusculus

all identical

ENSMUSG00000022041

256

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008002

257

Drerio

all identical

ENSDARG00000006602

257

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017553

237

protein features

start (aa)	end (aa)	feature	details
265	289	TRANSMEM	Helical; (Potential).	lost
297	315	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	352	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
353	502	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
503	521	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1590 / 1590

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

530 / 530

position of stopcodon in wt / mu cDNA

2199 / 2199

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

610 / 610

chromosome

strand

-1

last intron/exon boundary

2074

theoretical NMD boundary in CDS

1414

length of CDS

1590

coding sequence (CDS) position

836

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

1445

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

16277

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

27321124

original gDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered gDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

original cDNA sequence snippet

CATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGG

altered cDNA sequence snippet

CATCATCCCCTGCCTGCTCAACTCCTGCCTCACTGTGCTGG

wildtype AA sequence

mutated AA sequence

MGPSCPVFLS FTKLSLWWLL LTPAGGEEAK RPPPRAPGDP LSSPSPTALP QGGSHTETED
RLFKHLFRGY NRWARPVPNT SDVVIVRFGL SIAQLIDVDE KNQMMTTNVW LKQEWSDYKL
RWNPTDFGNI TSLRVPSEMI WIPDIVLYNN ADGEFAVTHM TKAHLFSTGT VHWVPPAIYK
SSCSIDVTFF PFDQQNCKMK FGSWTYDKAK IDLEQMEQTV DLKDYWESGE WAIVNATGTY
NSKKYDCCAE IYPDVTYAFV IRRLPLFYTI NLIIPCLLNS CLTVLVFYLP SDCGEKITLC
ISVLLSLTVF LLLITEIIPS TSLVIPLIGE YLLFTMIFVT LSIVITVFVL NVHHRSPSTH
TMPHWVRGAL LGCVPRWLLM NRPPPPVELC HPLRLKLSPS YHWLESNVDA EEREVVVEEE
DRWACAGHVA PSVGTLCSHG HLHSGASGPK AEALLQEGEL LLSPHMQKAL EGVHYIADHL
RSEDADSSVK EDWKYVAMVI DRIFLWLFII VCFLGTIGLF LPPFLAGMI*

speed

1.28 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

Problems