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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: ENST00000007735
MT speed 0 s - this script 2.83542 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KRT33Apolymorphism_automatic0.053338763704499simple_aaeA270Vsingle base exchangers12937519show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.946661236295501 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:39503163G>AN/A show variant in all transcripts   IGV
HGNC symbol KRT33A
Ensembl transcript ID ENST00000007735
Genbank transcript ID NM_004138
UniProt peptide O76009
alteration type single base exchange
alteration region CDS
DNA changes c.809C>T
cDNA.854C>T
g.3902C>T
AA changes A270V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 270
frameshift no
known variant Reference ID: rs12937519
databasehomozygous (A/A)heterozygousallele carriers
1000G2529731225
ExAC41702228826458
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.0530.02
3.4170.99
(flanking)0.5190.994
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      270VSSSEQLQSYQAEIIELRRTVNAL
mutated  not conserved    270VSSSEQLQSYQVEIIELRRTVNA
Ptroglodytes  not conserved  ENSPTRG00000009158  270VSSSEQLQSYQVEIIELRRTVNA
Mmulatta  all identical  ENSMMUG00000010754  270VSSAEQLQSYQAEIIELRRTVNA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000035592  270VSSSEQLQSCQAEIIELRRTVNA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
57363REGIONRod.lost
220363REGIONCoil 2.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1215 / 1215
position (AA) of stopcodon in wt / mu AA sequence 405 / 405
position of stopcodon in wt / mu cDNA 1260 / 1260
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 46 / 46
chromosome 17
strand -1
last intron/exon boundary 1143
theoretical NMD boundary in CDS 1047
length of CDS 1215
coding sequence (CDS) position 809
cDNA position
(for ins/del: last normal base / first normal base)		 854
gDNA position
(for ins/del: last normal base / first normal base)		 3902
chromosomal position
(for ins/del: last normal base / first normal base)		 39503163
original gDNA sequence snippet GCAGCTGCAGTCCTACCAGGCGGAGATCATCGAGCTGAGAC
altered gDNA sequence snippet GCAGCTGCAGTCCTACCAGGTGGAGATCATCGAGCTGAGAC
original cDNA sequence snippet GCAGCTGCAGTCCTACCAGGCGGAGATCATCGAGCTGAGAC
altered cDNA sequence snippet GCAGCTGCAGTCCTACCAGGTGGAGATCATCGAGCTGAGAC
wildtype AA sequence MSYSCGLPSL SCRTSCSSRP CVPPSCHGCT LPGACNIPAN VSNCNWFCEG SFNGSEKETM
QFLNDRLASY LEKVRQLERD NAELENLIRE RSQQQEPLVC ASYQSYFKTI EELQQKILCS
KSENARLVVQ IDNAKLASDD FRTKYETELS LRQLVESDIN GLRRILDELT LCRSDLEAQV
ESLKEELLCL KQNHEQEVNT LRCQLGDRLN VEVDAAPTVD LNQVLNETRS QYEALVETNR
REVEQWFATQ TEELNKQVVS SSEQLQSYQA EIIELRRTVN ALEIELQAQH NLRDSLENTL
TESEARYSSQ LSQVQRLITN VESQLAEIRS DLERQNQEYQ VLLDVRARLE CEINTYRSLL
ESEDCKLPSN PCATTNACDK STGPCISNPC GLRARCGPCN TFGY*
mutated AA sequence MSYSCGLPSL SCRTSCSSRP CVPPSCHGCT LPGACNIPAN VSNCNWFCEG SFNGSEKETM
QFLNDRLASY LEKVRQLERD NAELENLIRE RSQQQEPLVC ASYQSYFKTI EELQQKILCS
KSENARLVVQ IDNAKLASDD FRTKYETELS LRQLVESDIN GLRRILDELT LCRSDLEAQV
ESLKEELLCL KQNHEQEVNT LRCQLGDRLN VEVDAAPTVD LNQVLNETRS QYEALVETNR
REVEQWFATQ TEELNKQVVS SSEQLQSYQV EIIELRRTVN ALEIELQAQH NLRDSLENTL
TESEARYSSQ LSQVQRLITN VESQLAEIRS DLERQNQEYQ VLLDVRARLE CEINTYRSLL
ESEDCKLPSN PCATTNACDK STGPCISNPC GLRARCGPCN TFGY*
speed 0.83 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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Problems