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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: ENST00000301656
MT speed 0 s - this script 2.591548 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT27polymorphism_automatic0.1409966035762simple_aaeaffectedS52Tsingle base exchangers2469826show file

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.8590033964238 (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) chr17:38938591C>GN/A show variant in all transcripts   IGV
HGNC symbol KRT27
Ensembl transcript ID ENST00000301656
Genbank transcript ID NM_181537
UniProt peptide Q7Z3Y8
alteration type single base exchange
alteration region CDS
DNA changes c.155G>C
cDNA.196G>C
g.196G>C
AA changes S52T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 52
frameshift no
known variant Reference ID: rs2469826
databasehomozygous (G/G)heterozygousallele carriers
1000G24810471295
ExAC49512286527816
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.360.993
2.3641
(flanking)1.7121
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 increased188wt: 0.7121 / mu: 0.7213 (marginal change - not scored)wt: AGTGGCTTCTCTTGTGCTTTTGGGGGCAGCTCATCTGCAGG
mu: AGTGGCTTCTCTTGTGCTTTTGGGGGCACCTCATCTGCAGG		 tttt|GGGG
Acc increased203wt: 0.28 / mu: 0.75wt: GCTTTTGGGGGCAGCTCATCTGCAGGAGGCTATGGCGGAGG
mu: GCTTTTGGGGGCACCTCATCTGCAGGAGGCTATGGCGGAGG		 atct|GCAG
Donor gained1910.47mu: TTTGGGGGCACCTCA TGGG|ggca
distance from splice site 196
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      52IGSGFSCAFGGSSSAGGYGGGLGG
mutated  all conserved    52IGSGFSCAFGGTSSAGGYGG
Ptroglodytes  all identical  ENSPTRG00000009130  52IGSGFSCAFGGSSSAGGYGG
Mmulatta  all identical  ENSMMUG00000001497  52IGSGFSCAFGGSSSAGGYGG
Fcatus  all identical  ENSFCAG00000002017  52IGSGFSCAFGGSSPAGGYGG
Mmusculus  all identical  ENSMUSG00000017588  52IGSGFSCAFGGSSLAGG---
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000025338  57Y-----CGSVSGGAAGGLG
protein features
start (aa)end (aa)featuredetails 
183REGIONHead.lost
1382COMPBIASGly-rich.lost
84119REGIONCoil 1A.might get lost (downstream of altered splice site)
84395REGIONRod.might get lost (downstream of altered splice site)
120141REGIONLinker 1.might get lost (downstream of altered splice site)
142233REGIONCoil 1B.might get lost (downstream of altered splice site)
234256REGIONLinker 12.might get lost (downstream of altered splice site)
257395REGIONCoil 2.might get lost (downstream of altered splice site)
396459REGIONTail.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1380 / 1380
position (AA) of stopcodon in wt / mu AA sequence 460 / 460
position of stopcodon in wt / mu cDNA 1421 / 1421
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 42 / 42
chromosome 17
strand -1
last intron/exon boundary 1282
theoretical NMD boundary in CDS 1190
length of CDS 1380
coding sequence (CDS) position 155
cDNA position
(for ins/del: last normal base / first normal base)		 196
gDNA position
(for ins/del: last normal base / first normal base)		 196
chromosomal position
(for ins/del: last normal base / first normal base)		 38938591
original gDNA sequence snippet CTCTTGTGCTTTTGGGGGCAGCTCATCTGCAGGAGGCTATG
altered gDNA sequence snippet CTCTTGTGCTTTTGGGGGCACCTCATCTGCAGGAGGCTATG
original cDNA sequence snippet CTCTTGTGCTTTTGGGGGCAGCTCATCTGCAGGAGGCTATG
altered cDNA sequence snippet CTCTTGTGCTTTTGGGGGCACCTCATCTGCAGGAGGCTATG
wildtype AA sequence MSVRFSSTSR RLGSCGGTGS VRLSSGGAGF GAGNTCGVPG IGSGFSCAFG GSSSAGGYGG
GLGGGSASCA AFTGNEHGLL SGNEKVTMQN LNDRLASYLE NVRALEEANA DLEQKIKGWY
EKFGPGSCRG LDHDYSRYFP IIDELKNQII SATTSNAHVV LQNDNARLTA DDFRLKFENE
LALHQSVEAD INGLRRVLDE LTLCRTDLEI QLETLSEELA YLKKNHEEEM KALQCAAGGN
VNVEMNAAPG VDLTVLLNNM RAEYEALAEQ NRRDAEAWFN EKSASLQQQI SDDAGATTSA
RNELIEMKRT LQTLEIELQS LLATKHSLEC SLTETESNYC AQLAQIQAQI GALEEQLHQV
RTETEGQKLE YEQLLDIKVH LEKEIETYCL LIDGEDGSCS KSKGYGGPGN QTKDSSKTTI
VKTVVEEIDP RGKVLSSRVH TVEEKSTKVN NKNEQRVSS*
mutated AA sequence MSVRFSSTSR RLGSCGGTGS VRLSSGGAGF GAGNTCGVPG IGSGFSCAFG GTSSAGGYGG
GLGGGSASCA AFTGNEHGLL SGNEKVTMQN LNDRLASYLE NVRALEEANA DLEQKIKGWY
EKFGPGSCRG LDHDYSRYFP IIDELKNQII SATTSNAHVV LQNDNARLTA DDFRLKFENE
LALHQSVEAD INGLRRVLDE LTLCRTDLEI QLETLSEELA YLKKNHEEEM KALQCAAGGN
VNVEMNAAPG VDLTVLLNNM RAEYEALAEQ NRRDAEAWFN EKSASLQQQI SDDAGATTSA
RNELIEMKRT LQTLEIELQS LLATKHSLEC SLTETESNYC AQLAQIQAQI GALEEQLHQV
RTETEGQKLE YEQLLDIKVH LEKEIETYCL LIDGEDGSCS KSKGYGGPGN QTKDSSKTTI
VKTVVEEIDP RGKVLSSRVH TVEEKSTKVN NKNEQRVSS*
speed 0.53 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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