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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: ENST00000328827
MT speed 1.34 s - this script 6.903663 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PAWRpolymorphism_automatic0.00331539850173801simple_aaeP78Rsingle base exchangers8176805show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996684601498262 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM085047)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:80083792G>CN/A show variant in all transcripts   IGV
HGNC symbol PAWR
Ensembl transcript ID ENST00000328827
Genbank transcript ID NM_002583
UniProt peptide Q96IZ0
alteration type single base exchange
alteration region CDS
DNA changes c.233C>G
cDNA.606C>G
g.1086C>G
AA changes P78R Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS
78
frameshift no
known variant Reference ID: rs8176805
databasehomozygous (C/C)heterozygousallele carriers
1000G356581937
ExAC437

known disease mutation at this position, please check HGMD for details (HGMD ID CM085047)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4841
1.31
(flanking)0.4121
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 284
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78NELNNNLPGGAPAAPAVPGPGGVN
mutated  not conserved    78NELNNNLPGGARAAPAVPGPGGV
Ptroglodytes  all identical  ENSPTRG00000005250  78NELNNNLPGGAPAAPAVPGPGGV
Mmulatta  all identical  ENSMMUG00000015179  78NELNNNLPGGAPAAPAVPGPGGV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000035873  72SELNHG-PAGA-AAPAAPAPGAL
Ggallus  no alignment  ENSGALG00000010320  n/a
Trubripes  not conserved  ENSTRUG00000013694  80NCLPPSYPVARSSSGTALKEETH
Drerio  not conserved  ENSDARG00000045486  50RTTELNNNGSSSVNCVSSAPSYPVA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
49120COMPBIASAla-rich.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1023 / 1023
position (AA) of stopcodon in wt / mu AA sequence 341 / 341
position of stopcodon in wt / mu cDNA 1396 / 1396
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 374 / 374
chromosome 12
strand -1
last intron/exon boundary 1310
theoretical NMD boundary in CDS 886
length of CDS 1023
coding sequence (CDS) position 233
cDNA position
(for ins/del: last normal base / first normal base)
606
gDNA position
(for ins/del: last normal base / first normal base)
1086
chromosomal position
(for ins/del: last normal base / first normal base)
80083792
original gDNA sequence snippet CAACCTCCCGGGCGGCGCGCCGGCCGCACCTGCCGTCCCCG
altered gDNA sequence snippet CAACCTCCCGGGCGGCGCGCGGGCCGCACCTGCCGTCCCCG
original cDNA sequence snippet CAACCTCCCGGGCGGCGCGCCGGCCGCACCTGCCGTCCCCG
altered cDNA sequence snippet CAACCTCCCGGGCGGCGCGCGGGCCGCACCTGCCGTCCCCG
wildtype AA sequence MATGGYRTSS GLGGSTTDFL EEWKAKREKM RAKQNPPGPA PPGGGSSDAA GKPPAGALGT
PAAAAANELN NNLPGGAPAA PAVPGPGGVN CAVGSAMLTR AAPGPRRSED EPPAASASAA
PPPQRDEEEP DGVPEKGKSS GPSARKGKGQ IEKRKLREKR RSTGVVNIPA AECLDEYEDD
EAGQKERKRE DAITQQNTIQ NEAVNLLDPG SSYLLQEPPR TVSGRYKSTT SVSEEDVSSR
YSRTDRSGFP RYNRDANVSG TLVSSSTLEK KIEDLEKEVV RERQENLRLV RLMQDKEEMI
GKLKEEIDLL NRDLDDIEDE NEQLKQENKT LLKVVGQLTR *
mutated AA sequence MATGGYRTSS GLGGSTTDFL EEWKAKREKM RAKQNPPGPA PPGGGSSDAA GKPPAGALGT
PAAAAANELN NNLPGGARAA PAVPGPGGVN CAVGSAMLTR AAPGPRRSED EPPAASASAA
PPPQRDEEEP DGVPEKGKSS GPSARKGKGQ IEKRKLREKR RSTGVVNIPA AECLDEYEDD
EAGQKERKRE DAITQQNTIQ NEAVNLLDPG SSYLLQEPPR TVSGRYKSTT SVSEEDVSSR
YSRTDRSGFP RYNRDANVSG TLVSSSTLEK KIEDLEKEVV RERQENLRLV RLMQDKEEMI
GKLKEEIDLL NRDLDDIEDE NEQLKQENKT LLKVVGQLTR *
speed 1.34 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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