Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000398486
Querying Taster for transcript #2: ENST00000377755
MT speed 0 s - this script 5.143458 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT40polymorphism_automatic5.34957229625377e-08simple_aaeaffectedR235Hsingle base exchangers2010027show file
KRT40polymorphism_automatic5.34957229625377e-08simple_aaeaffectedR235Hsingle base exchangers2010027show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999946504277 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:39137387C>TN/A show variant in all transcripts   IGV
HGNC symbol KRT40
Ensembl transcript ID ENST00000398486
Genbank transcript ID N/A
UniProt peptide Q6A162
alteration type single base exchange
alteration region CDS
DNA changes c.704G>A
cDNA.865G>A
g.6001G>A
AA changes R235H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
235
frameshift no
known variant Reference ID: rs2010027
databasehomozygous (T/T)heterozygousallele carriers
1000G4269551381
ExAC59182093126849
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0850.016
-0.0360.023
(flanking)1.1390.304
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased6004wt: 0.6517 / mu: 0.6953 (marginal change - not scored)wt: GGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCCTCA
mu: GGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCCTCA
 gtga|ACAG
Acc marginally increased6002wt: 0.4078 / mu: 0.4209 (marginal change - not scored)wt: CAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCCT
mu: CAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCCT
 tcgt|GAAC
Donor increased6002wt: 0.39 / mu: 0.73wt: CTTCGTGAACAGCTT
mu: CTTCATGAACAGCTT
 TCGT|gaac
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235KKNHEEEVNLLREQLGDRLSVELD
mutated  not conserved    235KKNHEEEVNLLHEQLGD
Ptroglodytes  not conserved  ENSPTRG00000030928  235KKNHEEEVNLLHEQLGD
Mmulatta  all identical  ENSMMUG00000001142  235KKNHEEEVSLLRGQLGD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059169  235KKGHEEEVNLLREQLGD
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000069046  289RDAHQQEMVSLRGQMAGTVTVDV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
90396REGIONRod.lost
136236REGIONCoil 1B.lost
237252REGIONLinker 12.might get lost (downstream of altered splice site)
241241CONFLICTR -> C (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
253396REGIONCoil 2.might get lost (downstream of altered splice site)
338338SITEStutter.might get lost (downstream of altered splice site)
349349CONFLICTC -> R (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
397431REGIONTail.might get lost (downstream of altered splice site)
408408CONFLICTT -> I (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1296 / 1296
position (AA) of stopcodon in wt / mu AA sequence 432 / 432
position of stopcodon in wt / mu cDNA 1457 / 1457
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 17
strand -1
last intron/exon boundary 1358
theoretical NMD boundary in CDS 1146
length of CDS 1296
coding sequence (CDS) position 704
cDNA position
(for ins/del: last normal base / first normal base)
865
gDNA position
(for ins/del: last normal base / first normal base)
6001
chromosomal position
(for ins/del: last normal base / first normal base)
39137387
original gDNA sequence snippet TCAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCC
altered gDNA sequence snippet TCAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCC
original cDNA sequence snippet AGAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCC
altered cDNA sequence snippet AGAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCC
wildtype AA sequence MTSDCSSTHC SPESCGTASG CAPASSCSVE TACLPGTCAT SRCQTPSFLS RSRGLTGCLL
PCYFTGSCNS PCLVGNCAWC EDGVFTSNEK ETMQFLNDRL ASYLEKVRSL EETNAELESR
IQEQCEQDIP MVCPDYQRYF NTIEDLQQKI LCTKAENSRL AVQLDNCKLA TDDFKSKYES
ELSLRQLLEA DISSLHGILE ELTLCKSDLE AHVESLKEDL LCLKKNHEEE VNLLREQLGD
RLSVELDTAP TLDLNRVLDE MRCQCETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
mutated AA sequence MTSDCSSTHC SPESCGTASG CAPASSCSVE TACLPGTCAT SRCQTPSFLS RSRGLTGCLL
PCYFTGSCNS PCLVGNCAWC EDGVFTSNEK ETMQFLNDRL ASYLEKVRSL EETNAELESR
IQEQCEQDIP MVCPDYQRYF NTIEDLQQKI LCTKAENSRL AVQLDNCKLA TDDFKSKYES
ELSLRQLLEA DISSLHGILE ELTLCKSDLE AHVESLKEDL LCLKKNHEEE VNLLHEQLGD
RLSVELDTAP TLDLNRVLDE MRCQCETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
speed 1.65 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

polymorphism

Model: simple_aae, prob: 0.999999946504277 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:39137387C>TN/A show variant in all transcripts   IGV
HGNC symbol KRT40
Ensembl transcript ID ENST00000377755
Genbank transcript ID NM_182497
UniProt peptide Q6A162
alteration type single base exchange
alteration region CDS
DNA changes c.704G>A
cDNA.739G>A
g.6001G>A
AA changes R235H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
235
frameshift no
known variant Reference ID: rs2010027
databasehomozygous (T/T)heterozygousallele carriers
1000G4269551381
ExAC59182093126849
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0850.016
-0.0360.023
(flanking)1.1390.304
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased6004wt: 0.6517 / mu: 0.6953 (marginal change - not scored)wt: GGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCCTCA
mu: GGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCCTCA
 gtga|ACAG
Acc marginally increased6002wt: 0.4078 / mu: 0.4209 (marginal change - not scored)wt: CAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCCT
mu: CAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCCT
 tcgt|GAAC
Donor increased6002wt: 0.39 / mu: 0.73wt: CTTCGTGAACAGCTT
mu: CTTCATGAACAGCTT
 TCGT|gaac
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235KKNHEEEVNLLREQLGDRLSVELD
mutated  not conserved    235KKNHEEEVNLLHEQLGD
Ptroglodytes  not conserved  ENSPTRG00000030928  235KKNHEEEVNLLHEQLGD
Mmulatta  all identical  ENSMMUG00000001142  235KKNHEEEVSLLRGQLGD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059169  235KKGHEEEVNLLREQLGD
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000069046  289RDAHQQEMVSLRGQMAGTVTVDV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
90396REGIONRod.lost
136236REGIONCoil 1B.lost
237252REGIONLinker 12.might get lost (downstream of altered splice site)
241241CONFLICTR -> C (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
253396REGIONCoil 2.might get lost (downstream of altered splice site)
338338SITEStutter.might get lost (downstream of altered splice site)
349349CONFLICTC -> R (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
397431REGIONTail.might get lost (downstream of altered splice site)
408408CONFLICTT -> I (in Ref. 1; CAH10353).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1296 / 1296
position (AA) of stopcodon in wt / mu AA sequence 432 / 432
position of stopcodon in wt / mu cDNA 1331 / 1331
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 36 / 36
chromosome 17
strand -1
last intron/exon boundary 1232
theoretical NMD boundary in CDS 1146
length of CDS 1296
coding sequence (CDS) position 704
cDNA position
(for ins/del: last normal base / first normal base)
739
gDNA position
(for ins/del: last normal base / first normal base)
6001
chromosomal position
(for ins/del: last normal base / first normal base)
39137387
original gDNA sequence snippet TCAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCC
altered gDNA sequence snippet TCAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCC
original cDNA sequence snippet AGAGGAAGTCAACTTGCTTCGTGAACAGCTTGGCGACCGCC
altered cDNA sequence snippet AGAGGAAGTCAACTTGCTTCATGAACAGCTTGGCGACCGCC
wildtype AA sequence MTSDCSSTHC SPESCGTASG CAPASSCSVE TACLPGTCAT SRCQTPSFLS RSRGLTGCLL
PCYFTGSCNS PCLVGNCAWC EDGVFTSNEK ETMQFLNDRL ASYLEKVRSL EETNAELESR
IQEQCEQDIP MVCPDYQRYF NTIEDLQQKI LCTKAENSRL AVQLDNCKLA TDDFKSKYES
ELSLRQLLEA DISSLHGILE ELTLCKSDLE AHVESLKEDL LCLKKNHEEE VNLLREQLGD
RLSVELDTAP TLDLNRVLDE MRCQCETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
mutated AA sequence MTSDCSSTHC SPESCGTASG CAPASSCSVE TACLPGTCAT SRCQTPSFLS RSRGLTGCLL
PCYFTGSCNS PCLVGNCAWC EDGVFTSNEK ETMQFLNDRL ASYLEKVRSL EETNAELESR
IQEQCEQDIP MVCPDYQRYF NTIEDLQQKI LCTKAENSRL AVQLDNCKLA TDDFKSKYES
ELSLRQLLEA DISSLHGILE ELTLCKSDLE AHVESLKEDL LCLKKNHEEE VNLLHEQLGD
RLSVELDTAP TLDLNRVLDE MRCQCETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
speed 1.11 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