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 5.252072 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCH1disease_causing_automatic0.999999999076305simple_aaeaffected0M221Tsingle base exchangers104894434show file
GCH1disease_causing_automatic0.999999999076305simple_aaeaffected0M221Tsingle base exchangers104894434show file
GCH1disease_causing_automatic1without_aaeaffected0single base exchangers104894434show file
GCH1disease_causing_automatic1without_aaeaffected0single base exchangers104894434show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999076305 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM011358)
  • known disease mutation: rs9281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310826A>GN/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.662T>C
cDNA.851T>C
g.58745T>C
AA changes M221T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 221
frameshift no
known variant Reference ID: rs104894434
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs9281 (pathogenic for Intellectual disability|Autosomal recessive DOPA responsive dystonia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4491
5.0241
(flanking)5.0241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased58740wt: 0.43 / mu: 0.61wt: GTACAGAAAATGAAC
mu: GTACAGAAAACGAAC		 ACAG|aaaa
Donor marginally increased58739wt: 0.9869 / mu: 0.9874 (marginal change - not scored)wt: TGTACAGAAAATGAA
mu: TGTACAGAAAACGAA		 TACA|gaaa
Donor marginally increased58750wt: 0.9483 / mu: 0.9712 (marginal change - not scored)wt: TGAACAGCAAAACTG
mu: CGAACAGCAAAACTG		 AACA|gcaa
Donor marginally increased58745wt: 0.9216 / mu: 0.9491 (marginal change - not scored)wt: GAAAATGAACAGCAA
mu: GAAAACGAACAGCAA		 AAAT|gaac
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      221HMCMVMRGVQKMNSKTVTSTMLGV
mutated  not conserved    221HMCMVMRGVQKTNSKTVTSTMLG
Ptroglodytes  all identical  ENSPTRG00000006365  221HMCMVMRGVQKMNSKTVTSTMLG
Mmulatta  all identical  ENSMMUG00000004084  221HMCMVMRGVQKMNSKTVTSTMLG
Fcatus  all identical  ENSFCAG00000008872  106HMCMVMRGVQKMNSKTVTSTMLG
Mmusculus  all identical  ENSMUSG00000037580  212HMCMVMRGVQKMNSKTVTSTMLG
Ggallus  all identical  ENSGALG00000012200  207HMCMVMRGVQKMNSKTVTSTMLG
Trubripes  all identical  ENSTRUG00000015367  228HMCMVMRGVQKMNSKTVTSTMLG
Drerio  all identical  ENSDARG00000070453  222HMCMVMRGVQKMNSKTVTSTM
Dmelanogaster  all conserved  FBgn0003162  294HMCMVMRGVQKINSKTVTSTMLG
Celegans  all conserved  F32G8.6  193HMCMVMRGVQKINASTTTSCMLG
Xtropicalis  all identical  ENSXETG00000012214  218HMCMVMRGVQKMNSKTVTSTMLG
protein features
start (aa)end (aa)featuredetails 
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 662
cDNA position
(for ins/del: last normal base / first normal base)		 851
gDNA position
(for ins/del: last normal base / first normal base)		 58745
chromosomal position
(for ins/del: last normal base / first normal base)		 55310826
original gDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered gDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
original cDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered cDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
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 SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK TNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 1.20 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: 0.999999999076305 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM011358)
  • known disease mutation: rs9281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310826A>GN/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.662T>C
cDNA.823T>C
g.58745T>C
AA changes M221T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 221
frameshift no
known variant Reference ID: rs104894434
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs9281 (pathogenic for Intellectual disability|Autosomal recessive DOPA responsive dystonia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4491
5.0241
(flanking)5.0241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased58740wt: 0.43 / mu: 0.61wt: GTACAGAAAATGAAC
mu: GTACAGAAAACGAAC		 ACAG|aaaa
Donor marginally increased58739wt: 0.9869 / mu: 0.9874 (marginal change - not scored)wt: TGTACAGAAAATGAA
mu: TGTACAGAAAACGAA		 TACA|gaaa
Donor marginally increased58750wt: 0.9483 / mu: 0.9712 (marginal change - not scored)wt: TGAACAGCAAAACTG
mu: CGAACAGCAAAACTG		 AACA|gcaa
Donor marginally increased58745wt: 0.9216 / mu: 0.9491 (marginal change - not scored)wt: GAAAATGAACAGCAA
mu: GAAAACGAACAGCAA		 AAAT|gaac
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      221HMCMVMRGVQKMNSKTVTSTMLGV
mutated  not conserved    221HMCMVMRGVQKTNSKTVTSTMLG
Ptroglodytes  all identical  ENSPTRG00000006365  221HMCMVMRGVQKMNSKTVTSTMLG
Mmulatta  all identical  ENSMMUG00000004084  221HMCMVMRGVQKMNSKTVTSTMLG
Fcatus  all identical  ENSFCAG00000008872  106HMCMVMRGVQKMNSKTVTSTMLG
Mmusculus  all identical  ENSMUSG00000037580  212HMCMVMRGVQKMNSKTVTSTMLG
Ggallus  all identical  ENSGALG00000012200  207HMCMVMRGVQKMNSKTVTSTMLG
Trubripes  all identical  ENSTRUG00000015367  228HMCMVMRGVQKMNSKTVTSTMLG
Drerio  all identical  ENSDARG00000070453  222HMCMVMRGVQKMNSKTVTSTM
Dmelanogaster  all conserved  FBgn0003162  294HMCMVMRGVQKINSKTVTSTMLG
Celegans  all conserved  F32G8.6  193HMCMVMRGVQKINASTTTSCMLG
Xtropicalis  all identical  ENSXETG00000012214  218HMCMVMRGVQKMNSKTVTSTMLG
protein features
start (aa)end (aa)featuredetails 
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 662
cDNA position
(for ins/del: last normal base / first normal base)		 823
gDNA position
(for ins/del: last normal base / first normal base)		 58745
chromosomal position
(for ins/del: last normal base / first normal base)		 55310826
original gDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered gDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
original cDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered cDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
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 SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITEALRPA GVGVVVEATH MCMVMRGVQK TNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 1.14 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM011358)
  • known disease mutation: rs9281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310826A>GN/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 intron
DNA changes g.58745T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894434
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs9281 (pathogenic for Intellectual disability|Autosomal recessive DOPA responsive dystonia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4491
5.0241
(flanking)5.0241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased58740wt: 0.43 / mu: 0.61wt: GTACAGAAAATGAAC
mu: GTACAGAAAACGAAC		 ACAG|aaaa
Donor marginally increased58739wt: 0.9869 / mu: 0.9874 (marginal change - not scored)wt: TGTACAGAAAATGAA
mu: TGTACAGAAAACGAA		 TACA|gaaa
Donor marginally increased58750wt: 0.9483 / mu: 0.9712 (marginal change - not scored)wt: TGAACAGCAAAACTG
mu: CGAACAGCAAAACTG		 AACA|gcaa
Donor marginally increased58745wt: 0.9216 / mu: 0.9491 (marginal change - not scored)wt: GAAAATGAACAGCAA
mu: GAAAACGAACAGCAA		 AAAT|gaac
distance from splice site 239
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
202210STRANDmight 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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 58745
chromosomal position
(for ins/del: last normal base / first normal base)		 55310826
original gDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered gDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.28 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM011358)
  • known disease mutation: rs9281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55310826A>GN/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 intron
DNA changes g.58745T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894434
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs9281 (pathogenic for Intellectual disability|Autosomal recessive DOPA responsive dystonia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011358)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.4491
5.0241
(flanking)5.0241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased58740wt: 0.43 / mu: 0.61wt: GTACAGAAAATGAAC
mu: GTACAGAAAACGAAC		 ACAG|aaaa
Donor marginally increased58739wt: 0.9869 / mu: 0.9874 (marginal change - not scored)wt: TGTACAGAAAATGAA
mu: TGTACAGAAAACGAA		 TACA|gaaa
Donor marginally increased58750wt: 0.9483 / mu: 0.9712 (marginal change - not scored)wt: TGAACAGCAAAACTG
mu: CGAACAGCAAAACTG		 AACA|gcaa
Donor marginally increased58745wt: 0.9216 / mu: 0.9491 (marginal change - not scored)wt: GAAAATGAACAGCAA
mu: GAAAACGAACAGCAA		 AAAT|gaac
distance from splice site 1054
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
202210STRANDmight 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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 58745
chromosomal position
(for ins/del: last normal base / first normal base)		 55310826
original gDNA sequence snippet AATGCGAGGTGTACAGAAAATGAACAGCAAAACTGTGACCA
altered gDNA sequence snippet AATGCGAGGTGTACAGAAAACGAACAGCAAAACTGTGACCA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.89 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

Problems