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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000252252
MT speed 1.24 s - this script 7.217034 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT6Bpolymorphism_automatic1.516950236502e-05simple_aaeaffectedN21Ssingle base exchangers428894show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999984830497635 (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) chr12:52845801T>CN/A show variant in all transcripts   IGV
HGNC symbol KRT6B
Ensembl transcript ID ENST00000252252
Genbank transcript ID NM_005555
UniProt peptide P04259
alteration type single base exchange
alteration region CDS
DNA changes c.62A>G
cDNA.110A>G
g.110A>G
AA changes N21S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS
21
frameshift no
known variant Reference ID: rs428894
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC12309814920458
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8210.939
0.8950.831
(flanking)-1.1110.594
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained1090.96mu: GTGCCAGCTCAGCCA GCCA|gctc
distance from splice site 110
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      21SHSSSRRGFSANSARLPGVSRSGF
mutated  all conserved    21SHSSSRRGFSASSARLPGVSRSG
Ptroglodytes  all identical  ENSPTRG00000004979  21SHSSSRRGFSANSARLPGVSRSG
Mmulatta  not conserved  ENSMMUG00000018220  21SHSSSRRGFSAGSARLPGVSRSG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000058354  20SQTS-HRGYSASSARVPGLNRSG
Ggallus  not conserved  ENSGALG00000002349  20IQRG-RSGFSAASAIVPGTCRTS
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
2162REGIONHead.lost
6060MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
8990CONFLICTGS -> AG (in Ref. 2; AAA59466).might get lost (downstream of altered splice site)
116117CONFLICTAG -> PA (in Ref. 2; AAA59466).might get lost (downstream of altered splice site)
119121CONFLICTAGG -> LC (in Ref. 2; AAA59466).might get lost (downstream of altered splice site)
159160CONFLICTVR -> IG (in Ref. 2; AAA59466).might get lost (downstream of altered splice site)
163198REGIONCoil 1A.might get lost (downstream of altered splice site)
163472REGIONRod.might get lost (downstream of altered splice site)
199217REGIONLinker 1.might get lost (downstream of altered splice site)
218309REGIONCoil 1B.might get lost (downstream of altered splice site)
237237MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
255255CONFLICTD -> V (in Ref. 2; AAA59466).might get lost (downstream of altered splice site)
310333REGIONLinker 12.might get lost (downstream of altered splice site)
334472REGIONCoil 2.might get lost (downstream of altered splice site)
414414SITEStutter.might get lost (downstream of altered splice site)
473564REGIONTail.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1695 / 1695
position (AA) of stopcodon in wt / mu AA sequence 565 / 565
position of stopcodon in wt / mu cDNA 1743 / 1743
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 49 / 49
chromosome 12
strand -1
last intron/exon boundary 1508
theoretical NMD boundary in CDS 1409
length of CDS 1695
coding sequence (CDS) position 62
cDNA position
(for ins/del: last normal base / first normal base)
110
gDNA position
(for ins/del: last normal base / first normal base)
110
chromosomal position
(for ins/del: last normal base / first normal base)
52845801
original gDNA sequence snippet CCGCCGGGGTTTCAGTGCCAACTCAGCCAGGCTCCCTGGGG
altered gDNA sequence snippet CCGCCGGGGTTTCAGTGCCAGCTCAGCCAGGCTCCCTGGGG
original cDNA sequence snippet CCGCCGGGGTTTCAGTGCCAACTCAGCCAGGCTCCCTGGGG
altered cDNA sequence snippet CCGCCGGGGTTTCAGTGCCAGCTCAGCCAGGCTCCCTGGGG
wildtype AA sequence MASTSTTIRS HSSSRRGFSA NSARLPGVSR SGFSSISVSR SRGSGGLGGA CGGAGFGSRS
LYGLGGSKRI SIGGGSCAIS GGYGSRAGGS YGFGGAGSGF GFGGGAGIGF GLGGGAGLAG
GFGGPGFPVC PPGGIQEVTV NQSLLTPLNL QIDPAIQRVR AEEREQIKTL NNKFASFIDK
VRFLEQQNKV LDTKWTLLQE QGTKTVRQNL EPLFEQYINN LRRQLDNIVG ERGRLDSELR
NMQDLVEDLK NKYEDEINKR TAAENEFVTL KKDVDAAYMN KVELQAKADT LTDEINFLRA
LYDAELSQMQ THISDTSVVL SMDNNRNLDL DSIIAEVKAQ YEEIAQRSRA EAESWYQTKY
EELQITAGRH GDDLRNTKQE IAEINRMIQR LRSEIDHVKK QCANLQAAIA DAEQRGEMAL
KDAKNKLEGL EDALQKAKQD LARLLKEYQE LMNVKLALDV EIATYRKLLE GEECRLNGEG
VGQVNISVVQ STVSSGYGGA SGVGSGLGLG GGSSYSYGSG LGVGGGFSSS SGRATGGGLS
SVGGGSSTIK YTTTSSSSRK SYKH*
mutated AA sequence MASTSTTIRS HSSSRRGFSA SSARLPGVSR SGFSSISVSR SRGSGGLGGA CGGAGFGSRS
LYGLGGSKRI SIGGGSCAIS GGYGSRAGGS YGFGGAGSGF GFGGGAGIGF GLGGGAGLAG
GFGGPGFPVC PPGGIQEVTV NQSLLTPLNL QIDPAIQRVR AEEREQIKTL NNKFASFIDK
VRFLEQQNKV LDTKWTLLQE QGTKTVRQNL EPLFEQYINN LRRQLDNIVG ERGRLDSELR
NMQDLVEDLK NKYEDEINKR TAAENEFVTL KKDVDAAYMN KVELQAKADT LTDEINFLRA
LYDAELSQMQ THISDTSVVL SMDNNRNLDL DSIIAEVKAQ YEEIAQRSRA EAESWYQTKY
EELQITAGRH GDDLRNTKQE IAEINRMIQR LRSEIDHVKK QCANLQAAIA DAEQRGEMAL
KDAKNKLEGL EDALQKAKQD LARLLKEYQE LMNVKLALDV EIATYRKLLE GEECRLNGEG
VGQVNISVVQ STVSSGYGGA SGVGSGLGLG GGSSYSYGSG LGVGGGFSSS SGRATGGGLS
SVGGGSSTIK YTTTSSSSRK SYKH*
speed 1.24 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
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