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 5.203024 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCH1disease_causing0.999999999999924simple_aaeA196Ssingle base exchangers104894436show file
GCH1disease_causing0.999999999999924simple_aaeA196Ssingle base exchangers104894436show file
GCH1disease_causing0.999999999999924simple_aaeA196Ssingle base exchangers104894436show file
GCH1disease_causing0.999999999999924simple_aaeA196Ssingle base exchangers104894436show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999924      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012950)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55312526C>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.586G>T
cDNA.730G>T
g.57045G>T
AA changes A196S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 196
frameshift no
known variant Reference ID: rs104894436
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.4241
6.4241
(flanking)1.6211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      196LTKQIAVAITEALRPAGVGVVVEA
mutated  all conserved    196LTKQIAVAITESLRPAGVGVVVE
Ptroglodytes  all identical  ENSPTRG00000006365  196LTKQIAVAITEALRPAGVGVVVE
Mmulatta  all identical  ENSMMUG00000004084  196LTKQIAVAITEALRPAGVGVVVE
Fcatus  all identical  ENSFCAG00000008872  81LTKQIAVAITEALRPAGVGVVVE
Mmusculus  all identical  ENSMUSG00000037580  187VAITEALQPAGVGVVIE
Ggallus  all identical  ENSGALG00000012200  182ALQPAGVGVVIE
Trubripes  all identical  ENSTRUG00000015367  203LTKQIAVAITEALHPTGVGVVIE
Drerio  all identical  ENSDARG00000070453  197LTKQIAVAITEALQPAGVGVVVE
Dmelanogaster  all identical  FBgn0003162  269LTKQIAVAVTQAVQPAGVAVVVE
Celegans  all identical  F32G8.6  168LTKQIATAMVQAVQPSGVAVVIE
Xtropicalis  all identical  ENSXETG00000012214  193IAIAITEALHPSGVGVVVE
protein features
start (aa)end (aa)featuredetails 
182197HELIXlost
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 586
cDNA position
(for ins/del: last normal base / first normal base)		 730
gDNA position
(for ins/del: last normal base / first normal base)		 57045
chromosomal position
(for ins/del: last normal base / first normal base)		 55312526
original gDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered gDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
original cDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered cDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
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 SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITESLRPA GVGVVVEATK SNKYNKGLSP LLSSCHLFVA ILK*
speed 1.34 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: 0.999999999999924      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012950)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55312526C>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.586G>T
cDNA.775G>T
g.57045G>T
AA changes A196S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 196
frameshift no
known variant Reference ID: rs104894436
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.4241
6.4241
(flanking)1.6211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      196LTKQIAVAITEALRPAGVGVVVEA
mutated  all conserved    196LTKQIAVAITESLRPAGVGVVVE
Ptroglodytes  all identical  ENSPTRG00000006365  196LTKQIAVAITEALRPAGVGVVVE
Mmulatta  all identical  ENSMMUG00000004084  196LTKQIAVAITEALRPAGVGVVVE
Fcatus  all identical  ENSFCAG00000008872  81LTKQIAVAITEALRPAGVGVVVE
Mmusculus  all identical  ENSMUSG00000037580  187VAITEALQPAGVGVVIE
Ggallus  all identical  ENSGALG00000012200  182ALQPAGVGVVIE
Trubripes  all identical  ENSTRUG00000015367  203LTKQIAVAITEALHPTGVGVVIE
Drerio  all identical  ENSDARG00000070453  197LTKQIAVAITEALQPAGVGVVVE
Dmelanogaster  all identical  FBgn0003162  269LTKQIAVAVTQAVQPAGVAVVVE
Celegans  all identical  F32G8.6  168LTKQIATAMVQAVQPSGVAVVIE
Xtropicalis  all identical  ENSXETG00000012214  193IAIAITEALHPSGVGVVVE
protein features
start (aa)end (aa)featuredetails 
182197HELIXlost
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 586
cDNA position
(for ins/del: last normal base / first normal base)		 775
gDNA position
(for ins/del: last normal base / first normal base)		 57045
chromosomal position
(for ins/del: last normal base / first normal base)		 55312526
original gDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered gDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
original cDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered cDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
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 VAITESLRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 0.55 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: 0.999999999999924      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012950)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55312526C>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.586G>T
cDNA.739G>T
g.57045G>T
AA changes A196S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 196
frameshift no
known variant Reference ID: rs104894436
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.4241
6.4241
(flanking)1.6211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      196LTKQIAVAITEALRPAGVGVVVEA
mutated  all conserved    196LTKQIAVAITESLRPAGVGVVVE
Ptroglodytes  all identical  ENSPTRG00000006365  196LTKQIAVAITEALRPAGVGVVVE
Mmulatta  all identical  ENSMMUG00000004084  196LTKQIAVAITEALRPAGVGVVVE
Fcatus  all identical  ENSFCAG00000008872  81LTKQIAVAITEALRPAGVGVVVE
Mmusculus  all identical  ENSMUSG00000037580  187VAITEALQPAGVGVVIE
Ggallus  all identical  ENSGALG00000012200  182ALQPAGVGVVIE
Trubripes  all identical  ENSTRUG00000015367  203LTKQIAVAITEALHPTGVGVVIE
Drerio  all identical  ENSDARG00000070453  197LTKQIAVAITEALQPAGVGVVVE
Dmelanogaster  all identical  FBgn0003162  269LTKQIAVAVTQAVQPAGVAVVVE
Celegans  all identical  F32G8.6  168LTKQIATAMVQAVQPSGVAVVIE
Xtropicalis  all identical  ENSXETG00000012214  193IAIAITEALHPSGVGVVVE
protein features
start (aa)end (aa)featuredetails 
182197HELIXlost
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 586
cDNA position
(for ins/del: last normal base / first normal base)		 739
gDNA position
(for ins/del: last normal base / first normal base)		 57045
chromosomal position
(for ins/del: last normal base / first normal base)		 55312526
original gDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered gDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
original cDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered cDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
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 SLGENPQRQG LLKTPWRAAS AMQFFTKGYQ ETISDVLNDA
IFDEDHDEMV IVKDIDMFSM CEHHLVPFVG KVHIGYLPNK QVLGLSKLAR IVEIYSRRLQ
VQERLTKQIA VAITESLRPA GVGVVVEATS AEP*
speed 1.40 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: 0.999999999999924      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012950)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:55312526C>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.586G>T
cDNA.747G>T
g.57045G>T
AA changes A196S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 196
frameshift no
known variant Reference ID: rs104894436
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012950)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.4241
6.4241
(flanking)1.6211
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      196LTKQIAVAITEALRPAGVGVVVEA
mutated  all conserved    196LTKQIAVAITESLRPAGVGVVVE
Ptroglodytes  all identical  ENSPTRG00000006365  196LTKQIAVAITEALRPAGVGVVVE
Mmulatta  all identical  ENSMMUG00000004084  196LTKQIAVAITEALRPAGVGVVVE
Fcatus  all identical  ENSFCAG00000008872  81LTKQIAVAITEALRPAGVGVVVE
Mmusculus  all identical  ENSMUSG00000037580  187VAITEALQPAGVGVVIE
Ggallus  all identical  ENSGALG00000012200  182ALQPAGVGVVIE
Trubripes  all identical  ENSTRUG00000015367  203LTKQIAVAITEALHPTGVGVVIE
Drerio  all identical  ENSDARG00000070453  197LTKQIAVAITEALQPAGVGVVVE
Dmelanogaster  all identical  FBgn0003162  269LTKQIAVAVTQAVQPAGVAVVVE
Celegans  all identical  F32G8.6  168LTKQIATAMVQAVQPSGVAVVIE
Xtropicalis  all identical  ENSXETG00000012214  193IAIAITEALHPSGVGVVVE
protein features
start (aa)end (aa)featuredetails 
182197HELIXlost
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 586
cDNA position
(for ins/del: last normal base / first normal base)		 747
gDNA position
(for ins/del: last normal base / first normal base)		 57045
chromosomal position
(for ins/del: last normal base / first normal base)		 55312526
original gDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered gDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
original cDNA sequence snippet TTGCTGTAGCAATCACGGAAGCCTTGCGGCCTGCTGGAGTC
altered cDNA sequence snippet TTGCTGTAGCAATCACGGAATCCTTGCGGCCTGCTGGAGTC
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 VAITESLRPA GVGVVVEATH MCMVMRGVQK MNSKTVTSTM LGVFREDPKT
REEFLTLIRS *
speed 0.47 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

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