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 2.96 s - this script 4.865243 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT40polymorphism_automatic0.021287597982162simple_aaeaffectedC265Ysingle base exchangers721957show file
KRT40polymorphism_automatic0.021287597982162simple_aaeaffectedC265Ysingle base exchangers721957show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.978712402017838 (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) chr17:39137297C>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.794G>A
cDNA.955G>A
g.6091G>A
AA changes C265Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
265
frameshift no
known variant Reference ID: rs721957
databasehomozygous (T/T)heterozygousallele carriers
1000G12689392207
ExAC22404-1204110363
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0290.991
3.3361
(flanking)4.8731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6094wt: 0.22 / mu: 0.38wt: TGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACAATC
mu: TGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACAATC
 gtga|AACG
Donor marginally increased6092wt: 0.8876 / mu: 0.9661 (marginal change - not scored)wt: CAGTGTGAAACGGTG
mu: CAGTATGAAACGGTG
 GTGT|gaaa
distance from splice site 56
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      265LNRVLDEMRCQCETVLANNRREAE
mutated  not conserved    265LNRVLDEMRCQYETVLANNRREA
Ptroglodytes  not conserved  ENSPTRG00000030928  265LNRVLDEMRCQYETVLANNRREA
Mmulatta  not conserved  ENSMMUG00000001142  265LNRVLDEMRCQYETVLANNRREA
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000059169  265LNKVLDEMRCQYERVLANNRRDA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000069046  319LSRVIAEIRSEYET
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
90396REGIONRod.lost
253396REGIONCoil 2.lost
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 794
cDNA position
(for ins/del: last normal base / first normal base)
955
gDNA position
(for ins/del: last normal base / first normal base)
6091
chromosomal position
(for ins/del: last normal base / first normal base)
39137297
original gDNA sequence snippet GGATGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACA
altered gDNA sequence snippet GGATGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACA
original cDNA sequence snippet GGATGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACA
altered cDNA sequence snippet GGATGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACA
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 VNLLREQLGD
RLSVELDTAP TLDLNRVLDE MRCQYETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
speed 1.51 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: 0.978712402017838 (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) chr17:39137297C>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.794G>A
cDNA.829G>A
g.6091G>A
AA changes C265Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
265
frameshift no
known variant Reference ID: rs721957
databasehomozygous (T/T)heterozygousallele carriers
1000G12689392207
ExAC22404-1204110363
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0290.991
3.3361
(flanking)4.8731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6094wt: 0.22 / mu: 0.38wt: TGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACAATC
mu: TGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACAATC
 gtga|AACG
Donor marginally increased6092wt: 0.8876 / mu: 0.9661 (marginal change - not scored)wt: CAGTGTGAAACGGTG
mu: CAGTATGAAACGGTG
 GTGT|gaaa
distance from splice site 56
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      265LNRVLDEMRCQCETVLANNRREAE
mutated  not conserved    265LNRVLDEMRCQYETVLANNRREA
Ptroglodytes  not conserved  ENSPTRG00000030928  265LNRVLDEMRCQYETVLANNRREA
Mmulatta  not conserved  ENSMMUG00000001142  265LNRVLDEMRCQYETVLANNRREA
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000059169  265LNKVLDEMRCQYERVLANNRRDA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000069046  319LSRVIAEIRSEYET
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
90396REGIONRod.lost
253396REGIONCoil 2.lost
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 794
cDNA position
(for ins/del: last normal base / first normal base)
829
gDNA position
(for ins/del: last normal base / first normal base)
6091
chromosomal position
(for ins/del: last normal base / first normal base)
39137297
original gDNA sequence snippet GGATGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACA
altered gDNA sequence snippet GGATGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACA
original cDNA sequence snippet GGATGAGATGCGCTGTCAGTGTGAAACGGTGCTTGCCAACA
altered cDNA sequence snippet GGATGAGATGCGCTGTCAGTATGAAACGGTGCTTGCCAACA
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 VNLLREQLGD
RLSVELDTAP TLDLNRVLDE MRCQYETVLA NNRREAEEWL AVQTEELNQQ QLSSAEQLQG
CQMEILELKR TASALEIELQ AQQSLTESLE CTVAETEAQY SSQLAQIQCL IDNLENQLAE
IRCDLERQNQ EYQVLLDVKA RLEGEINTYW GLLDSEDSRL SCSPCSTTCT SSNTCEPCSA
YVICTVENCC L*
speed 1.45 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

Problems