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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: ENST00000380293
MT speed 0 s - this script 2.863231 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AVPdisease_causing_automatic0.999998588199642simple_aaeaffected0C92Ysingle base exchangers121964891show file

Taster files

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Prediction

disease causing

 Model: simple_aae, prob: 0.999998588199642 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960146)
  • known disease mutation at this position (HGMD CM980199)
  • known disease mutation: rs12217 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:3063670C>TN/A show variant in all transcripts   IGV
HGNC symbol AVP
Ensembl transcript ID ENST00000380293
Genbank transcript ID NM_000490
UniProt peptide P01185
alteration type single base exchange
alteration region CDS
DNA changes c.275G>A
cDNA.325G>A
g.1701G>A
AA changes C92Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 92
frameshift no
known variant Reference ID: rs121964891
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12217 (pathogenic for Neurohypophyseal diabetes insipidus) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960146)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980199)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3571
5.6161
(flanking)3.2110.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1706wt: 0.32 / mu: 0.48wt: GCGGGAGCGGGGGCC
mu: ACGGGAGCGGGGGCC		 GGGA|gcgg
Donor gained17030.47mu: CGTACGGGAGCGGGG TACG|ggag
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      92LPSPCQSGQKACGSGGRCAAFGVC
mutated  not conserved    92LPSPCQSGQKAYGSGGRCAAFGV
Ptroglodytes  all identical  ENSPTRG00000013190  92LPSPCQSGQKACGSGGRCAAFGV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000037727  96LPSPCQSGQKPCGSGGRCAAVGI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058567  96LSGPCETGGTSCGDRGGRCAAEGI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
9292DISULFIDBy similarity.lost
9898DISULFIDBy similarity.might get lost (downstream of altered splice site)
104104DISULFIDBy similarity.might get lost (downstream of altered splice site)
105105DISULFIDBy similarity.might get lost (downstream of altered splice site)
110110DISULFIDBy similarity.might get lost (downstream of altered splice site)
116116DISULFIDBy similarity.might get lost (downstream of altered splice site)
126164PEPTIDECopeptin. /FTId=PRO_0000020517.might get lost (downstream of altered splice site)
131131CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 495 / 495
position (AA) of stopcodon in wt / mu AA sequence 165 / 165
position of stopcodon in wt / mu cDNA 545 / 545
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 51 / 51
chromosome 20
strand -1
last intron/exon boundary 373
theoretical NMD boundary in CDS 272
length of CDS 495
coding sequence (CDS) position 275
cDNA position
(for ins/del: last normal base / first normal base)		 325
gDNA position
(for ins/del: last normal base / first normal base)		 1701
chromosomal position
(for ins/del: last normal base / first normal base)		 3063670
original gDNA sequence snippet CCAGTCCGGCCAGAAGGCGTGCGGGAGCGGGGGCCGCTGCG
altered gDNA sequence snippet CCAGTCCGGCCAGAAGGCGTACGGGAGCGGGGGCCGCTGCG
original cDNA sequence snippet CCAGTCCGGCCAGAAGGCGTGCGGGAGCGGGGGCCGCTGCG
altered cDNA sequence snippet CCAGTCCGGCCAGAAGGCGTACGGGAGCGGGGGCCGCTGCG
wildtype AA sequence MPDTMLPACF LGLLAFSSAC YFQNCPRGGK RAMSDLELRQ CLPCGPGGKG RCFGPSICCA
DELGCFVGTA EALRCQEENY LPSPCQSGQK ACGSGGRCAA FGVCCNDESC VTEPECREGF
HRRARASDRS NATQLDGPAG ALLLRLVQLA GAPEPFEPAQ PDAY*
mutated AA sequence MPDTMLPACF LGLLAFSSAC YFQNCPRGGK RAMSDLELRQ CLPCGPGGKG RCFGPSICCA
DELGCFVGTA EALRCQEENY LPSPCQSGQK AYGSGGRCAA FGVCCNDESC VTEPECREGF
HRRARASDRS NATQLDGPAG ALLLRLVQLA GAPEPFEPAQ PDAY*
speed 0.76 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