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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000348749
Querying Taster for transcript #2: ENST00000261007
Querying Taster for transcript #3: ENST00000409542
Querying Taster for transcript #4: ENST00000409219
MT speed 4.1 s - this script 5.312762 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNA1	disease_causing_automatic	0.999999999468507	simple_aae		affected	0	F194L	single base exchange	rs137852806		show file
CHRNA1	disease_causing_automatic	0.999999999698137	simple_aae		affected	0	F301L	single base exchange	rs137852806		show file
CHRNA1	disease_causing_automatic	0.999999999698137	simple_aae		affected	0	F276L	single base exchange	rs137852806		show file
CHRNA1	disease_causing_automatic	0.999999999698137	simple_aae		affected	0	F276L	single base exchange	rs137852806		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999468507 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040988)
known disease mutation: rs18384 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175614850A>GN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000409542

Genbank transcript ID

N/A

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.580T>C
cDNA.598T>C
g.14351T>C

AA changes

F194L Score: 22 explain score(s)

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

194

frameshift

known variant

Reference ID: rs137852806
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18384 (pathogenic for Congenital myasthenic syndrome 1B, fast-channel) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040988)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040988)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040988)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.074	1
	5.074	1
(flanking)	3.435	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	14348	wt: 0.6721 / mu: 0.7106 (marginal change - not scored)	wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG mu: CTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTG	actg\|TGTT
Acc marginally increased	14345	wt: 0.7643 / mu: 0.7979 (marginal change - not scored)	wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC mu: TCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATC	ttga\|CTGT
Acc marginally increased	14347	wt: 0.6568 / mu: 0.6819 (marginal change - not scored)	wt: TCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGT mu: TCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGT	gact\|GTGT
Acc increased	14344	wt: 0.41 / mu: 0.48	wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT mu: ATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCAT	tttg\|ACTG
Acc marginally increased	14358	wt: 0.8010 / mu: 0.8535 (marginal change - not scored)	wt: GTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCC mu: GTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAGCTGATCC	ttct\|GGTC
Acc marginally increased	14343	wt: 0.9704 / mu: 0.9754 (marginal change - not scored)	wt: CATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCA mu: CATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCA	cttt\|GACT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

194

mutated

not conserved

194

Ptroglodytes

all identical

ENSPTRG00000012658

301

Mmulatta

all identical

ENSMMUG00000021796

300

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

276

Ggallus

all identical

ENSGALG00000009301

286

Trubripes

all identical

ENSTRUG00000008738

297

Drerio

all identical

ENSDARG00000009021

276

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

310

Xtropicalis

all identical

ENSXETG00000025418

276

protein features

start (aa)	end (aa)	feature	details
21	255	TOPO_DOM	Extracellular.	lost
237	237	DISULFID	Associated with receptor activation.	might get lost (downstream of altered splice site)
238	238	DISULFID	Associated with receptor activation.	might get lost (downstream of altered splice site)
256	280	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
288	306	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
322	341	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
342	453	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
415	415	CONFLICT	P -> F (in Ref. 4; AAD14247).	might get lost (downstream of altered splice site)
454	472	TRANSMEM	Helical.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1128 / 1128

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

376 / 376

position of stopcodon in wt / mu cDNA

1146 / 1146

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

19 / 19

chromosome

strand

-1

last intron/exon boundary

1015

theoretical NMD boundary in CDS

946

length of CDS

1128

coding sequence (CDS) position

580

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

598

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

14351

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

175614850

original gDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered gDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

original cDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered cDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

wildtype AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVLLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*

speed

0.37 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: 0.999999999698137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040988)
known disease mutation: rs18384 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175614850A>GN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000261007

Genbank transcript ID

NM_001039523

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.901T>C
cDNA.968T>C
g.14351T>C

AA changes

F301L Score: 22 explain score(s)

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

301

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.074	1
	5.074	1
(flanking)	3.435	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	14348	wt: 0.6721 / mu: 0.7106 (marginal change - not scored)	wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG mu: CTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTG	actg\|TGTT
Acc marginally increased	14345	wt: 0.7643 / mu: 0.7979 (marginal change - not scored)	wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC mu: TCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATC	ttga\|CTGT
Acc marginally increased	14347	wt: 0.6568 / mu: 0.6819 (marginal change - not scored)	wt: TCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGT mu: TCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGT	gact\|GTGT
Acc increased	14344	wt: 0.41 / mu: 0.48	wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT mu: ATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCAT	tttg\|ACTG
Acc marginally increased	14358	wt: 0.8010 / mu: 0.8535 (marginal change - not scored)	wt: GTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCC mu: GTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAGCTGATCC	ttct\|GGTC
Acc marginally increased	14343	wt: 0.9704 / mu: 0.9754 (marginal change - not scored)	wt: CATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCA mu: CATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCA	cttt\|GACT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

301

mutated

not conserved

301

Ptroglodytes

all identical

ENSPTRG00000012658

301

Mmulatta

all identical

ENSMMUG00000021796

300

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

276

Ggallus

all identical

ENSGALG00000009301

286

Trubripes

all identical

ENSTRUG00000008738

297

Drerio

all identical

ENSDARG00000009021

276

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

310

Xtropicalis

all identical

ENSXETG00000025418

276

protein features

start (aa)	end (aa)	feature	details
288	306	TRANSMEM	Helical.	lost
322	341	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
342	453	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
415	415	CONFLICT	P -> F (in Ref. 4; AAD14247).	might get lost (downstream of altered splice site)
454	472	TRANSMEM	Helical.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1449 / 1449

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

483 / 483

position of stopcodon in wt / mu cDNA

1516 / 1516

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

68 / 68

chromosome

strand

-1

last intron/exon boundary

1385

theoretical NMD boundary in CDS

1267

length of CDS

1449

coding sequence (CDS) position

901

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

968

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

14351

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

175614850

original gDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered gDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

original cDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered cDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

wildtype AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV VAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLTV
FLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV VAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLTV
LLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*

speed

1.32 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999698137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040988)
known disease mutation: rs18384 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175614850A>GN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000348749

Genbank transcript ID

NM_000079

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.826T>C
cDNA.904T>C
g.14351T>C

AA changes

F276L Score: 22 explain score(s)

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

276

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.074	1
	5.074	1
(flanking)	3.435	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	14348	wt: 0.6721 / mu: 0.7106 (marginal change - not scored)	wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG mu: CTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTG	actg\|TGTT
Acc marginally increased	14345	wt: 0.7643 / mu: 0.7979 (marginal change - not scored)	wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC mu: TCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATC	ttga\|CTGT
Acc marginally increased	14347	wt: 0.6568 / mu: 0.6819 (marginal change - not scored)	wt: TCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGT mu: TCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGT	gact\|GTGT
Acc increased	14344	wt: 0.41 / mu: 0.48	wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT mu: ATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCAT	tttg\|ACTG
Acc marginally increased	14358	wt: 0.8010 / mu: 0.8535 (marginal change - not scored)	wt: GTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCC mu: GTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAGCTGATCC	ttct\|GGTC
Acc marginally increased	14343	wt: 0.9704 / mu: 0.9754 (marginal change - not scored)	wt: CATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCA mu: CATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCA	cttt\|GACT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

276

mutated

not conserved

276

Ptroglodytes

all identical

ENSPTRG00000012658

301

Mmulatta

all identical

ENSMMUG00000021796

300

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

276

Ggallus

all identical

ENSGALG00000009301

286

Trubripes

all identical

ENSTRUG00000008738

297

Drerio

all identical

ENSDARG00000009021

276

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

310

Xtropicalis

all identical

ENSXETG00000025418

276

protein features

start (aa)	end (aa)	feature	details
256	280	TRANSMEM	Helical.	lost
288	306	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
322	341	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
342	453	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
415	415	CONFLICT	P -> F (in Ref. 4; AAD14247).	might get lost (downstream of altered splice site)
454	472	TRANSMEM	Helical.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1374 / 1374

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

458 / 458

position of stopcodon in wt / mu cDNA

1452 / 1452

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

79 / 79

chromosome

strand

-1

last intron/exon boundary

1321

theoretical NMD boundary in CDS

1192

length of CDS

1374

coding sequence (CDS) position

826

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

904

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

14351

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

175614850

original gDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered gDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

original cDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered cDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

wildtype AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVLLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*

speed

1.05 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999698137 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM040988)
known disease mutation: rs18384 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:175614850A>GN/A show variant in all transcripts IGV

HGNC symbol

CHRNA1

Ensembl transcript ID

ENST00000409219

Genbank transcript ID

N/A

UniProt peptide

P02708

alteration type

single base exchange

alteration region

CDS

DNA changes

c.826T>C
cDNA.844T>C
g.14351T>C

AA changes

F276L Score: 22 explain score(s)

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

276

frameshift

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.074	1
	5.074	1
(flanking)	3.435	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	14348	wt: 0.6721 / mu: 0.7106 (marginal change - not scored)	wt: CTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTG mu: CTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTG	actg\|TGTT
Acc marginally increased	14345	wt: 0.7643 / mu: 0.7979 (marginal change - not scored)	wt: TCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATC mu: TCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATC	ttga\|CTGT
Acc marginally increased	14347	wt: 0.6568 / mu: 0.6819 (marginal change - not scored)	wt: TCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGT mu: TCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGT	gact\|GTGT
Acc increased	14344	wt: 0.41 / mu: 0.48	wt: ATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCAT mu: ATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCAT	tttg\|ACTG
Acc marginally increased	14358	wt: 0.8010 / mu: 0.8535 (marginal change - not scored)	wt: GTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAGCTGATCC mu: GTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAGCTGATCC	ttct\|GGTC
Acc marginally increased	14343	wt: 0.9704 / mu: 0.9754 (marginal change - not scored)	wt: CATCTCTGTCTTACTGTCTTTGACTGTGTTCCTTCTGGTCA mu: CATCTCTGTCTTACTGTCTTTGACTGTGCTCCTTCTGGTCA	cttt\|GACT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

276

mutated

not conserved

276

Ptroglodytes

all identical

ENSPTRG00000012658

301

Mmulatta

all identical

ENSMMUG00000021796

300

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000027107

276

Ggallus

all identical

ENSGALG00000009301

286

Trubripes

all identical

ENSTRUG00000008738

297

Drerio

all identical

ENSDARG00000009021

276

Dmelanogaster

no homologue

Celegans

all identical

K11G12.2

310

Xtropicalis

all identical

ENSXETG00000025418

276

protein features

start (aa)	end (aa)	feature	details
256	280	TRANSMEM	Helical.	lost
288	306	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
322	341	TRANSMEM	Helical.	might get lost (downstream of altered splice site)
342	453	TOPO_DOM	Cytoplasmic.	might get lost (downstream of altered splice site)
415	415	CONFLICT	P -> F (in Ref. 4; AAD14247).	might get lost (downstream of altered splice site)
454	472	TRANSMEM	Helical.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1134 / 1134

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

378 / 378

position of stopcodon in wt / mu cDNA

1152 / 1152

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

19 / 19

chromosome

strand

-1

last intron/exon boundary

1021

theoretical NMD boundary in CDS

952

length of CDS

1134

coding sequence (CDS) position

826

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

844

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

14351

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

175614850

original gDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered gDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

original cDNA sequence snippet

TCTTACTGTCTTTGACTGTGTTCCTTCTGGTCATCGTGGAG

altered cDNA sequence snippet

TCTTACTGTCTTTGACTGTGCTCCTTCTGGTCATCGTGGAG

wildtype AA sequence

mutated AA sequence

MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVLLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*

speed

1.36 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

Problems