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: ENST00000389494
Querying Taster for transcript #2: ENST00000389492
Querying Taster for transcript #3: ENST00000541596
MT speed 0 s - this script 3.925285 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHRNG	disease_causing_automatic	0.999999955430048	simple_aae		affected	0	R187C	single base exchange	rs121912670		show file
CHRNG	disease_causing_automatic	0.999999955430048	simple_aae		affected	0	R239C	single base exchange	rs121912670		show file
CHRNG	disease_causing_automatic	0.999999955430048	simple_aae		affected	0	R239C	single base exchange	rs121912670		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999955430048 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062516)
known disease mutation: rs18337 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:233407702C>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNG

Ensembl transcript ID

ENST00000389492

Genbank transcript ID

N/A

UniProt peptide

P07510

alteration type

single base exchange

alteration region

CDS

DNA changes

c.559C>T
cDNA.559C>T
g.3266C>T

AA changes

R187C Score: 180 explain score(s)

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

187

frameshift

known variant

Reference ID: rs121912670

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

known disease mutation: rs18337 (pathogenic for Lethal multiple pterygium syndrome|Autosomal recessive multiple pterygium syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM062516)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062516)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062516)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.757	1
	2.185	1
(flanking)	6.017	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 increased	3264	wt: 0.44 / mu: 0.66	wt: GGTGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACG mu: GGTGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACG	tcca\|GCGC
Acc increased	3270	wt: 0.32 / mu: 0.47	wt: CTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTCATCA mu: CTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTCATCA	gcaa\|GCCC
Donor marginally increased	3264	wt: 0.5376 / mu: 0.5391 (marginal change - not scored)	wt: CATCCAGCGCAAGCC mu: CATCCAGTGCAAGCC	TCCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

187

mutated

not conserved

187

Ptroglodytes

all identical

ENSPTRG00000022726

239

Mmulatta

all identical

ENSMMUG00000022149

243

Fcatus

all identical

ENSFCAG00000005681

159

Mmusculus

all identical

ENSMUSG00000026253

239

Ggallus

all identical

ENSGALG00000007906

241

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086647

244

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	240	TOPO_DOM	Extracellular (Potential).	lost
241	265	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
275	293	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
285	285	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
309	330	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	474	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
475	495	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

1398 / 1398

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

466 / 466

position of stopcodon in wt / mu cDNA

1398 / 1398

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

1 / 1

chromosome

strand

last intron/exon boundary

1225

theoretical NMD boundary in CDS

1174

length of CDS

1398

coding sequence (CDS) position

559

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

559

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

3266

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

233407702

original gDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered gDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

original cDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered cDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

wildtype AA sequence

MHGGQGPLLL LLLLAVCLGA QGRNQEERLL ADLMQNYDPN LRPAERDSDV VNVSLKLTLT
NLISLNEREE ALTTNVWIEM QWCDYRLRWD PRDYEGLWVL RVPSTMVWRP DIVLENKSQT
YSTNEIDLQL SQEDGQTIEW IFIDPEAFTE NGEWAIQHRP AKMLLDPAAP AQEAGHQKVV
FYLLIQRKPL FYVINIIAPC VLISSVAILI HFLPAKAGGQ KCTVAINVLL AQTVFLFLVA
KKVPETSQAV PLISKYLTFL LVVTILIVVN AVVVLNVSLR SPHTHSMARG VRKVFLRLLP
QLLRMHVRPL APAAVQDTQS RLQNGSSGWS ITTGEEVALC LPRSELLFQQ WQRQGLVAAA
LEKLEKGPEL GLSQFCGSLK QAAPAIQACV EACNLIACAR HQQSHFDNGN EEWFLVGRVL
DRVCFLAMLS LFICGTAGIF LMAHYNRVPA LPFPGDPRPY LPSPD*

mutated AA sequence

MHGGQGPLLL LLLLAVCLGA QGRNQEERLL ADLMQNYDPN LRPAERDSDV VNVSLKLTLT
NLISLNEREE ALTTNVWIEM QWCDYRLRWD PRDYEGLWVL RVPSTMVWRP DIVLENKSQT
YSTNEIDLQL SQEDGQTIEW IFIDPEAFTE NGEWAIQHRP AKMLLDPAAP AQEAGHQKVV
FYLLIQCKPL FYVINIIAPC VLISSVAILI HFLPAKAGGQ KCTVAINVLL AQTVFLFLVA
KKVPETSQAV PLISKYLTFL LVVTILIVVN AVVVLNVSLR SPHTHSMARG VRKVFLRLLP
QLLRMHVRPL APAAVQDTQS RLQNGSSGWS ITTGEEVALC LPRSELLFQQ WQRQGLVAAA
LEKLEKGPEL GLSQFCGSLK QAAPAIQACV EACNLIACAR HQQSHFDNGN EEWFLVGRVL
DRVCFLAMLS LFICGTAGIF LMAHYNRVPA LPFPGDPRPY LPSPD*

speed

0.56 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: 0.999999955430048 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062516)
known disease mutation: rs18337 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:233407702C>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNG

Ensembl transcript ID

ENST00000389494

Genbank transcript ID

NM_005199

UniProt peptide

P07510

alteration type

single base exchange

alteration region

CDS

DNA changes

c.715C>T
cDNA.736C>T
g.3266C>T

AA changes

R239C Score: 180 explain score(s)

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

239

frameshift

known variant

Reference ID: rs121912670

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

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.757	1
	2.185	1
(flanking)	6.017	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 increased	3264	wt: 0.44 / mu: 0.66	wt: GGTGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACG mu: GGTGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACG	tcca\|GCGC
Acc increased	3270	wt: 0.32 / mu: 0.47	wt: CTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTCATCA mu: CTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTCATCA	gcaa\|GCCC
Donor marginally increased	3264	wt: 0.5376 / mu: 0.5391 (marginal change - not scored)	wt: CATCCAGCGCAAGCC mu: CATCCAGTGCAAGCC	TCCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

239

mutated

not conserved

239

Ptroglodytes

all identical

ENSPTRG00000022726

239

Mmulatta

all identical

ENSMMUG00000022149

243

Fcatus

all identical

ENSFCAG00000005681

159

Mmusculus

all identical

ENSMUSG00000026253

239

Ggallus

all identical

ENSGALG00000007906

241

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086647

244

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	240	TOPO_DOM	Extracellular (Potential).	lost
241	265	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
275	293	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
285	285	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
309	330	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	474	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
475	495	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

1554 / 1554

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

518 / 518

position of stopcodon in wt / mu cDNA

1575 / 1575

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

22 / 22

chromosome

strand

last intron/exon boundary

1402

theoretical NMD boundary in CDS

1330

length of CDS

1554

coding sequence (CDS) position

715

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

736

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

3266

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

233407702

original gDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered gDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

original cDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered cDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

wildtype AA sequence

MHGGQGPLLL LLLLAVCLGA QGRNQEERLL ADLMQNYDPN LRPAERDSDV VNVSLKLTLT
NLISLNEREE ALTTNVWIEM QWCDYRLRWD PRDYEGLWVL RVPSTMVWRP DIVLENNVDG
VFEVALYCNV LVSPDGCIYW LPPAIFRSAC SISVTYFPFD WQNCSLIFQS QTYSTNEIDL
QLSQEDGQTI EWIFIDPEAF TENGEWAIQH RPAKMLLDPA APAQEAGHQK VVFYLLIQRK
PLFYVINIIA PCVLISSVAI LIHFLPAKAG GQKCTVAINV LLAQTVFLFL VAKKVPETSQ
AVPLISKYLT FLLVVTILIV VNAVVVLNVS LRSPHTHSMA RGVRKVFLRL LPQLLRMHVR
PLAPAAVQDT QSRLQNGSSG WSITTGEEVA LCLPRSELLF QQWQRQGLVA AALEKLEKGP
ELGLSQFCGS LKQAAPAIQA CVEACNLIAC ARHQQSHFDN GNEEWFLVGR VLDRVCFLAM
LSLFICGTAG IFLMAHYNRV PALPFPGDPR PYLPSPD*

mutated AA sequence

MHGGQGPLLL LLLLAVCLGA QGRNQEERLL ADLMQNYDPN LRPAERDSDV VNVSLKLTLT
NLISLNEREE ALTTNVWIEM QWCDYRLRWD PRDYEGLWVL RVPSTMVWRP DIVLENNVDG
VFEVALYCNV LVSPDGCIYW LPPAIFRSAC SISVTYFPFD WQNCSLIFQS QTYSTNEIDL
QLSQEDGQTI EWIFIDPEAF TENGEWAIQH RPAKMLLDPA APAQEAGHQK VVFYLLIQCK
PLFYVINIIA PCVLISSVAI LIHFLPAKAG GQKCTVAINV LLAQTVFLFL VAKKVPETSQ
AVPLISKYLT FLLVVTILIV VNAVVVLNVS LRSPHTHSMA RGVRKVFLRL LPQLLRMHVR
PLAPAAVQDT QSRLQNGSSG WSITTGEEVA LCLPRSELLF QQWQRQGLVA AALEKLEKGP
ELGLSQFCGS LKQAAPAIQA CVEACNLIAC ARHQQSHFDN GNEEWFLVGR VLDRVCFLAM
LSLFICGTAG IFLMAHYNRV PALPFPGDPR PYLPSPD*

speed

0.52 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999955430048 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062516)
known disease mutation: rs18337 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:233407702C>TN/A show variant in all transcripts IGV

HGNC symbol

CHRNG

Ensembl transcript ID

ENST00000541596

Genbank transcript ID

NM_005199

UniProt peptide

P07510

alteration type

single base exchange

alteration region

CDS

DNA changes

c.715C>T
cDNA.736C>T
g.3266C>T

AA changes

R239C Score: 180 explain score(s)

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

239

frameshift

known variant

Reference ID: rs121912670

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

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.757	1
	2.185	1
(flanking)	6.017	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 increased	3264	wt: 0.44 / mu: 0.66	wt: GGTGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACG mu: GGTGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACG	tcca\|GCGC
Acc increased	3270	wt: 0.32 / mu: 0.47	wt: CTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTCATCA mu: CTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTCATCA	gcaa\|GCCC
Donor marginally increased	3264	wt: 0.5376 / mu: 0.5391 (marginal change - not scored)	wt: CATCCAGCGCAAGCC mu: CATCCAGTGCAAGCC	TCCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

239

mutated

not conserved

239

Ptroglodytes

all identical

ENSPTRG00000022726

239

Mmulatta

all identical

ENSMMUG00000022149

243

Fcatus

all identical

ENSFCAG00000005681

159

Mmusculus

all identical

ENSMUSG00000026253

239

Ggallus

all identical

ENSGALG00000007906

241

Trubripes

no homologue

Drerio

all identical

ENSDARG00000086647

244

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
23	240	TOPO_DOM	Extracellular (Potential).	lost
241	265	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
275	293	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
285	285	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
309	330	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
331	474	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
475	495	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

1554 / 1554

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

518 / 518

position of stopcodon in wt / mu cDNA

1575 / 1575

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

22 / 22

chromosome

strand

last intron/exon boundary

2264

theoretical NMD boundary in CDS

2192

length of CDS

1554

coding sequence (CDS) position

715

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

736

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

3266

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

233407702

original gDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered gDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

original cDNA sequence snippet

TGTTCTACCTGCTCATCCAGCGCAAGCCCCTCTTCTACGTC

altered cDNA sequence snippet

TGTTCTACCTGCTCATCCAGTGCAAGCCCCTCTTCTACGTC

wildtype AA sequence

mutated AA sequence

MHGGQGPLLL LLLLAVCLGA QGRNQEERLL ADLMQNYDPN LRPAERDSDV VNVSLKLTLT
NLISLNEREE ALTTNVWIEM QWCDYRLRWD PRDYEGLWVL RVPSTMVWRP DIVLENNVDG
VFEVALYCNV LVSPDGCIYW LPPAIFRSAC SISVTYFPFD WQNCSLIFQS QTYSTNEIDL
QLSQEDGQTI EWIFIDPEAF TENGEWAIQH RPAKMLLDPA APAQEAGHQK VVFYLLIQCK
PLFYVINIIA PCVLISSVAI LIHFLPAKAG GQKCTVAINV LLAQTVFLFL VAKKVPETSQ
AVPLISKYLT FLLVVTILIV VNAVVVLNVS LRSPHTHSMA RGVRKVFLRL LPQLLRMHVR
PLAPAAVQDT QSRLQNGSSG WSITTGEEVA LCLPRSELLF QQWQRQGLVA AALEKLEKGP
ELGLSQFCGS LKQAAPAIQA CVEACNLIAC ARHQQSHFDN GNEEWFLVGR VLDRVCFLAM
LSLFICGTAG IFLMAHYNRV PALPFPGDPR PYLPSPD*

speed

1.05 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