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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000398486
Querying Taster for transcript #2: ENST00000377755
MT speed 0 s - this script 3.7813 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT40polymorphism_automatic6.29496454962464e-14simple_aaeaffectedT37Asingle base exchangers1510069show file
KRT40polymorphism_automatic6.29496454962464e-14simple_aaeaffectedT37Asingle base exchangers1510069show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999937 (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) chr17:39140417T>CN/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.109A>G
cDNA.270A>G
g.2971A>G
AA changes T37A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 37
frameshift no
known variant Reference ID: rs1510069
databasehomozygous (C/C)heterozygousallele carriers
1000G4269561382
ExAC59042095926863
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3480
-1.5210
(flanking)-1.1560
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2969wt: 0.59 / mu: 0.68wt: GGAAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGAT
mu: GGAAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGAT		 ccgg|TACC
Acc marginally increased2972wt: 0.2160 / mu: 0.2204 (marginal change - not scored)wt: AACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGTC
mu: AACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGTC		 gtac|CTGT
Acc increased2967wt: 0.35 / mu: 0.44wt: GTGGAAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCG
mu: GTGGAAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCG		 cccc|GGTA
distance from splice site 110
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      37SCSVETACLPGTCATSRCQTPSFL
mutated  not conserved    37SCSVETACLPGACATSRCQTPSF
Ptroglodytes  not conserved  ENSPTRG00000030928  37SCSVETACLPGACATSRCQTPSF
Mmulatta  not conserved  ENSMMUG00000001142  37SCCIETACLPGACATSRCQTPSF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059169  37FCPTNTTCLPNTCSTSRCQTPSF
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000069046  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
189REGIONHead.lost
90124REGIONCoil 1A.might get lost (downstream of altered splice site)
90396REGIONRod.might get lost (downstream of altered splice site)
125135REGIONLinker 1.might get lost (downstream of altered splice site)
136236REGIONCoil 1B.might get lost (downstream of altered splice site)
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 109
cDNA position
(for ins/del: last normal base / first normal base)		 270
gDNA position
(for ins/del: last normal base / first normal base)		 2971
chromosomal position
(for ins/del: last normal base / first normal base)		 39140417
original gDNA sequence snippet AAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGT
altered gDNA sequence snippet AAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGT
original cDNA sequence snippet AAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGT
altered cDNA sequence snippet AAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGT
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 TACLPGACAT 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*
speed 0.98 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: 0.999999999999937 (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) chr17:39140417T>CN/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.109A>G
cDNA.144A>G
g.2971A>G
AA changes T37A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 37
frameshift no
known variant Reference ID: rs1510069
databasehomozygous (C/C)heterozygousallele carriers
1000G4269561382
ExAC59042095926863
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3480
-1.5210
(flanking)-1.1560
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2969wt: 0.59 / mu: 0.68wt: GGAAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGAT
mu: GGAAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGAT		 ccgg|TACC
Acc marginally increased2972wt: 0.2160 / mu: 0.2204 (marginal change - not scored)wt: AACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGTC
mu: AACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGTC		 gtac|CTGT
Acc increased2967wt: 0.35 / mu: 0.44wt: GTGGAAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCG
mu: GTGGAAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCG		 cccc|GGTA
distance from splice site 144
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      37SCSVETACLPGTCATSRCQTPSFL
mutated  not conserved    37SCSVETACLPGACATSRCQTPSF
Ptroglodytes  not conserved  ENSPTRG00000030928  37SCSVETACLPGACATSRCQTPSF
Mmulatta  not conserved  ENSMMUG00000001142  37SCCIETACLPGACATSRCQTPSF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000059169  37FCPTNTTCLPNTCSTSRCQTPSF
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000069046  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
189REGIONHead.lost
90124REGIONCoil 1A.might get lost (downstream of altered splice site)
90396REGIONRod.might get lost (downstream of altered splice site)
125135REGIONLinker 1.might get lost (downstream of altered splice site)
136236REGIONCoil 1B.might get lost (downstream of altered splice site)
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 109
cDNA position
(for ins/del: last normal base / first normal base)		 144
gDNA position
(for ins/del: last normal base / first normal base)		 2971
chromosomal position
(for ins/del: last normal base / first normal base)		 39140417
original gDNA sequence snippet AAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGT
altered gDNA sequence snippet AAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGT
original cDNA sequence snippet AAACAGCTTGTCTCCCCGGTACCTGTGCTACATCCCGATGT
altered cDNA sequence snippet AAACAGCTTGTCTCCCCGGTGCCTGTGCTACATCCCGATGT
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 TACLPGACAT 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*
speed 0.80 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