Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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: ENST00000543643
Querying Taster for transcript #2: ENST00000491895
Querying Taster for transcript #3: ENST00000536224
Querying Taster for transcript #4: ENST00000395514
MT speed 0 s - this script 4.130948 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCH1disease_causing_automatic0.999999993469589simple_aaeaffected0R88Wsingle base exchangers104894433show file
GCH1disease_causing_automatic0.999999993469589simple_aaeaffected0R88Wsingle base exchangers104894433show file
GCH1disease_causing_automatic0.999999993469589simple_aaeaffected0R88Wsingle base exchangers104894433show file
GCH1disease_causing_automatic0.999999993469589simple_aaeaffected0R88Wsingle base exchangers104894433show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993469589 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050621)
  • known disease mutation at this position (HGMD CM940820)
  • known disease mutation: rs9271 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55369120G>AN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000543643
Genbank transcript ID NM_001024070
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.262C>T
cDNA.406C>T
g.451C>T
AA changes R88W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs104894433
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs9271 (pathogenic for Dystonia 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3031
1.181
(flanking)1.1580.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained4440.36mu: GAGAACCCCCAGTGG GAAC|cccc
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88SILSSLGENPQRQGLLKTPWRAAS
mutated  not conserved    88SILSSLGENPQWQGLLKTPWRAA
Ptroglodytes  all identical  ENSPTRG00000006365  88SILSSLGENPQRQGLLKTPWRAA
Mmulatta  all identical  ENSMMUG00000004084  88SILSSLGENPQRQGLLKTPWRAA
Fcatus  no alignment  ENSFCAG00000008872  n/a
Mmusculus  all identical  ENSMUSG00000037580  79SILLSLGEDPQRQGLLKTPWRAA
Ggallus  all identical  ENSGALG00000012200  74TILRALGEDPERQGLLKTPWRAA
Trubripes  all identical  ENSTRUG00000015367  95RQGLLKTPWRAA
Drerio  all identical  ENSDARG00000070453  89TILRGLGEDPQRQGLLKTPWRAA
Dmelanogaster  all identical  FBgn0003162  161LLLGGLGENPDRQGLIKTPERAA
Celegans  all identical  F32G8.6  60SIIQHVGEDINRQGLLKTPERAA
Xtropicalis  all identical  ENSXETG00000012214  85TILRALGEDPGRQGLLKTPWRAA
protein features
start (aa)end (aa)featuredetails 
9193HELIXmight get lost (downstream of altered splice site)
94102HELIXmight get lost (downstream of altered splice site)
103106TURNmight get lost (downstream of altered splice site)
108110HELIXmight get lost (downstream of altered splice site)
113115TURNmight get lost (downstream of altered splice site)
130141STRANDmight get lost (downstream of altered splice site)
141141METALZinc.might get lost (downstream of altered splice site)
142144TURNmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
147156STRANDmight get lost (downstream of altered splice site)
165176HELIXmight get lost (downstream of altered splice site)
177180STRANDmight get lost (downstream of altered splice site)
182197HELIXmight get lost (downstream of altered splice site)
202210STRANDmight get lost (downstream of altered splice site)
206206CONFLICTV -> I (in Ref. 9; CAA78908).might get lost (downstream of altered splice site)
211214HELIXmight get lost (downstream of altered splice site)
212212METALZinc.might get lost (downstream of altered splice site)
215217TURNmight get lost (downstream of altered splice site)
224230STRANDmight get lost (downstream of altered splice site)
233236HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 702 / 702
position (AA) of stopcodon in wt / mu AA sequence 234 / 234
position of stopcodon in wt / mu cDNA 846 / 846
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 145 / 145
chromosome 14
strand -1
last intron/exon boundary 859
theoretical NMD boundary in CDS 664
length of CDS 702
coding sequence (CDS) position 262
cDNA position
(for ins/del: last normal base / first normal base)		 406
gDNA position
(for ins/del: last normal base / first normal base)		 451
chromosomal position
(for ins/del: last normal base / first normal base)		 55369120
original gDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered gDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
original cDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered cDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATK SNKYNKGLSP LLSSCHLFVA ILK*
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQWQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATK SNKYNKGLSP LLSSCHLFVA ILK*
speed 0.68 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993469589 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050621)
  • known disease mutation at this position (HGMD CM940820)
  • known disease mutation: rs9271 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55369120G>AN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000491895
Genbank transcript ID NM_000161
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.262C>T
cDNA.451C>T
g.451C>T
AA changes R88W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs104894433
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs9271 (pathogenic for Dystonia 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3031
1.181
(flanking)1.1580.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained4440.36mu: GAGAACCCCCAGTGG GAAC|cccc
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88SILSSLGENPQRQGLLKTPWRAAS
mutated  not conserved    88SILSSLGENPQWQGLLKTPWRAA
Ptroglodytes  all identical  ENSPTRG00000006365  88SILSSLGENPQRQGLLKTPWRAA
Mmulatta  all identical  ENSMMUG00000004084  88SILSSLGENPQRQGLLKTPWRAA
Fcatus  no alignment  ENSFCAG00000008872  n/a
Mmusculus  all identical  ENSMUSG00000037580  79SILLSLGEDPQRQGLLKTPWRAA
Ggallus  all identical  ENSGALG00000012200  74TILRALGEDPERQGLLKTPWRAA
Trubripes  all identical  ENSTRUG00000015367  95RQGLLKTPWRAA
Drerio  all identical  ENSDARG00000070453  89TILRGLGEDPQRQGLLKTPWRAA
Dmelanogaster  all identical  FBgn0003162  161LLLGGLGENPDRQGLIKTPERAA
Celegans  all identical  F32G8.6  60SIIQHVGEDINRQGLLKTPERAA
Xtropicalis  all identical  ENSXETG00000012214  85TILRALGEDPGRQGLLKTPWRAA
protein features
start (aa)end (aa)featuredetails 
9193HELIXmight get lost (downstream of altered splice site)
94102HELIXmight get lost (downstream of altered splice site)
103106TURNmight get lost (downstream of altered splice site)
108110HELIXmight get lost (downstream of altered splice site)
113115TURNmight get lost (downstream of altered splice site)
130141STRANDmight get lost (downstream of altered splice site)
141141METALZinc.might get lost (downstream of altered splice site)
142144TURNmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
147156STRANDmight get lost (downstream of altered splice site)
165176HELIXmight get lost (downstream of altered splice site)
177180STRANDmight get lost (downstream of altered splice site)
182197HELIXmight get lost (downstream of altered splice site)
202210STRANDmight get lost (downstream of altered splice site)
206206CONFLICTV -> I (in Ref. 9; CAA78908).might get lost (downstream of altered splice site)
211214HELIXmight get lost (downstream of altered splice site)
212212METALZinc.might get lost (downstream of altered splice site)
215217TURNmight get lost (downstream of altered splice site)
224230STRANDmight get lost (downstream of altered splice site)
233236HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 753 / 753
position (AA) of stopcodon in wt / mu AA sequence 251 / 251
position of stopcodon in wt / mu cDNA 942 / 942
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 190 / 190
chromosome 14
strand -1
last intron/exon boundary 816
theoretical NMD boundary in CDS 576
length of CDS 753
coding sequence (CDS) position 262
cDNA position
(for ins/del: last normal base / first normal base)		 451
gDNA position
(for ins/del: last normal base / first normal base)		 451
chromosomal position
(for ins/del: last normal base / first normal base)		 55369120
original gDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered gDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
original cDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered cDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQWQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 0.45 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993469589 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050621)
  • known disease mutation at this position (HGMD CM940820)
  • known disease mutation: rs9271 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55369120G>AN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000536224
Genbank transcript ID NM_001024071
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.262C>T
cDNA.415C>T
g.451C>T
AA changes R88W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs104894433
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs9271 (pathogenic for Dystonia 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3031
1.181
(flanking)1.1580.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained4440.36mu: GAGAACCCCCAGTGG GAAC|cccc
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88SILSSLGENPQRQGLLKTPWRAAS
mutated  not conserved    88SILSSLGENPQWQGLLKTPWRAA
Ptroglodytes  all identical  ENSPTRG00000006365  88SILSSLGENPQRQGLLKTPWRAA
Mmulatta  all identical  ENSMMUG00000004084  88SILSSLGENPQRQGLLKTPWRAA
Fcatus  no alignment  ENSFCAG00000008872  n/a
Mmusculus  all identical  ENSMUSG00000037580  79SILLSLGEDPQRQGLLKTPWRAA
Ggallus  all identical  ENSGALG00000012200  74TILRALGEDPERQGLLKTPWRAA
Trubripes  all identical  ENSTRUG00000015367  95RQGLLKTPWRAA
Drerio  all identical  ENSDARG00000070453  89TILRGLGEDPQRQGLLKTPWRAA
Dmelanogaster  all identical  FBgn0003162  161LLLGGLGENPDRQGLIKTPERAA
Celegans  all identical  F32G8.6  60SIIQHVGEDINRQGLLKTPERAA
Xtropicalis  all identical  ENSXETG00000012214  85TILRALGEDPGRQGLLKTPWRAA
protein features
start (aa)end (aa)featuredetails 
9193HELIXmight get lost (downstream of altered splice site)
94102HELIXmight get lost (downstream of altered splice site)
103106TURNmight get lost (downstream of altered splice site)
108110HELIXmight get lost (downstream of altered splice site)
113115TURNmight get lost (downstream of altered splice site)
130141STRANDmight get lost (downstream of altered splice site)
141141METALZinc.might get lost (downstream of altered splice site)
142144TURNmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
147156STRANDmight get lost (downstream of altered splice site)
165176HELIXmight get lost (downstream of altered splice site)
177180STRANDmight get lost (downstream of altered splice site)
182197HELIXmight get lost (downstream of altered splice site)
202210STRANDmight get lost (downstream of altered splice site)
206206CONFLICTV -> I (in Ref. 9; CAA78908).might get lost (downstream of altered splice site)
211214HELIXmight get lost (downstream of altered splice site)
212212METALZinc.might get lost (downstream of altered splice site)
215217TURNmight get lost (downstream of altered splice site)
224230STRANDmight get lost (downstream of altered splice site)
233236HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 642 / 642
position (AA) of stopcodon in wt / mu AA sequence 214 / 214
position of stopcodon in wt / mu cDNA 795 / 795
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 154 / 154
chromosome 14
strand -1
last intron/exon boundary 780
theoretical NMD boundary in CDS 576
length of CDS 642
coding sequence (CDS) position 262
cDNA position
(for ins/del: last normal base / first normal base)		 415
gDNA position
(for ins/del: last normal base / first normal base)		 451
chromosomal position
(for ins/del: last normal base / first normal base)		 55369120
original gDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered gDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
original cDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered cDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATS AEP*
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQWQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATS AEP*
speed 0.93 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993469589 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050621)
  • known disease mutation at this position (HGMD CM940820)
  • known disease mutation: rs9271 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55369120G>AN/A show variant in all transcripts   IGV
HGNC symbol GCH1
Ensembl transcript ID ENST00000395514
Genbank transcript ID NM_001024024
UniProt peptide P30793
alteration type single base exchange
alteration region CDS
DNA changes c.262C>T
cDNA.423C>T
g.451C>T
AA changes R88W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs104894433
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs9271 (pathogenic for Dystonia 5) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940820)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
ZEB1, Transcription Factor, ZEB1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3031
1.181
(flanking)1.1580.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained4440.36mu: GAGAACCCCCAGTGG GAAC|cccc
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88SILSSLGENPQRQGLLKTPWRAAS
mutated  not conserved    88SILSSLGENPQWQGLLKTPWRAA
Ptroglodytes  all identical  ENSPTRG00000006365  88SILSSLGENPQRQGLLKTPWRAA
Mmulatta  all identical  ENSMMUG00000004084  88SILSSLGENPQRQGLLKTPWRAA
Fcatus  no alignment  ENSFCAG00000008872  n/a
Mmusculus  all identical  ENSMUSG00000037580  79SILLSLGEDPQRQGLLKTPWRAA
Ggallus  all identical  ENSGALG00000012200  74TILRALGEDPERQGLLKTPWRAA
Trubripes  all identical  ENSTRUG00000015367  95RQGLLKTPWRAA
Drerio  all identical  ENSDARG00000070453  89TILRGLGEDPQRQGLLKTPWRAA
Dmelanogaster  all identical  FBgn0003162  161LLLGGLGENPDRQGLIKTPERAA
Celegans  all identical  F32G8.6  60SIIQHVGEDINRQGLLKTPERAA
Xtropicalis  all identical  ENSXETG00000012214  85TILRALGEDPGRQGLLKTPWRAA
protein features
start (aa)end (aa)featuredetails 
9193HELIXmight get lost (downstream of altered splice site)
94102HELIXmight get lost (downstream of altered splice site)
103106TURNmight get lost (downstream of altered splice site)
108110HELIXmight get lost (downstream of altered splice site)
113115TURNmight get lost (downstream of altered splice site)
130141STRANDmight get lost (downstream of altered splice site)
141141METALZinc.might get lost (downstream of altered splice site)
142144TURNmight get lost (downstream of altered splice site)
144144METALZinc.might get lost (downstream of altered splice site)
147156STRANDmight get lost (downstream of altered splice site)
165176HELIXmight get lost (downstream of altered splice site)
177180STRANDmight get lost (downstream of altered splice site)
182197HELIXmight get lost (downstream of altered splice site)
202210STRANDmight get lost (downstream of altered splice site)
206206CONFLICTV -> I (in Ref. 9; CAA78908).might get lost (downstream of altered splice site)
211214HELIXmight get lost (downstream of altered splice site)
212212METALZinc.might get lost (downstream of altered splice site)
215217TURNmight get lost (downstream of altered splice site)
224230STRANDmight get lost (downstream of altered splice site)
233236HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 753 / 753
position (AA) of stopcodon in wt / mu AA sequence 251 / 251
position of stopcodon in wt / mu cDNA 914 / 914
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 162 / 162
chromosome 14
strand -1
last intron/exon boundary 931
theoretical NMD boundary in CDS 719
length of CDS 753
coding sequence (CDS) position 262
cDNA position
(for ins/del: last normal base / first normal base)		 423
gDNA position
(for ins/del: last normal base / first normal base)		 451
chromosomal position
(for ins/del: last normal base / first normal base)		 55369120
original gDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered gDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
original cDNA sequence snippet CGCTGGGCGAGAACCCCCAGCGGCAAGGGCTGCTCAAGACG
altered cDNA sequence snippet CGCTGGGCGAGAACCCCCAGTGGCAAGGGCTGCTCAAGACG
wildtype AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
mutated AA sequence MEKGPVRAPA EKPRGARCSN GFPERDPPRP GPSRPAEKPP RPEAKSAQPA DGWKGERPRS
EEDNELNLPN LAAAYSSILS SLGENPQWQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 0.27 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
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Problems