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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 2.52826 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AVPdisease_causing_automatic0.99334286915873simple_aaeaffected0G88Ssingle base exchangers121964882show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.99334286915873 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910064)
  • known disease mutation at this position (HGMD CM960147)
  • known disease mutation: rs12204 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:3063683C>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.262G>A
cDNA.312G>A
g.1688G>A
AA changes G88S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs121964882
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12204 (pathogenic for Neurohypophyseal diabetes insipidus) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960147)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960147)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960147)
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)3.4661
3.450.996
(flanking)-2.4350.082
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 increased1679wt: 0.2478 / mu: 0.2695 (marginal change - not scored)wt: AGAACTACCTGCCGTCGCCCTGCCAGTCCGGCCAGAAGGCG
mu: AGAACTACCTGCCGTCGCCCTGCCAGTCCAGCCAGAAGGCG		 ccct|GCCA
Acc marginally increased1683wt: 0.9574 / mu: 0.9606 (marginal change - not scored)wt: CTACCTGCCGTCGCCCTGCCAGTCCGGCCAGAAGGCGTGCG
mu: CTACCTGCCGTCGCCCTGCCAGTCCAGCCAGAAGGCGTGCG		 gcca|GTCC
Donor increased1693wt: 0.38 / mu: 0.62wt: GGCCAGAAGGCGTGC
mu: AGCCAGAAGGCGTGC		 CCAG|aagg
Donor increased1683wt: 0.41 / mu: 0.98wt: CTGCCAGTCCGGCCA
mu: CTGCCAGTCCAGCCA		 GCCA|gtcc
Donor marginally increased1690wt: 0.9107 / mu: 0.9692 (marginal change - not scored)wt: TCCGGCCAGAAGGCG
mu: TCCAGCCAGAAGGCG		 CGGC|caga
Donor gained16880.86mu: AGTCCAGCCAGAAGG TCCA|gcca
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88EENYLPSPCQSGQKACGSGGRCAA
mutated  not conserved    88EENYLPSPCQSSQKACGSGGRCA
Ptroglodytes  all identical  ENSPTRG00000013190  88EENYLPSPCQSGQKACGSGGRCA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000037727  92EENYLPSPCQSGQKPCGSGGRCA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058567  92EEEQLSGPCETGGTSCGDRGGRCA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
9292DISULFIDBy similarity.might get lost (downstream of altered splice site)
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 262
cDNA position
(for ins/del: last normal base / first normal base)		 312
gDNA position
(for ins/del: last normal base / first normal base)		 1688
chromosomal position
(for ins/del: last normal base / first normal base)		 3063683
original gDNA sequence snippet TGCCGTCGCCCTGCCAGTCCGGCCAGAAGGCGTGCGGGAGC
altered gDNA sequence snippet TGCCGTCGCCCTGCCAGTCCAGCCAGAAGGCGTGCGGGAGC
original cDNA sequence snippet TGCCGTCGCCCTGCCAGTCCGGCCAGAAGGCGTGCGGGAGC
altered cDNA sequence snippet TGCCGTCGCCCTGCCAGTCCAGCCAGAAGGCGTGCGGGAGC
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 LPSPCQSSQK ACGSGGRCAA FGVCCNDESC VTEPECREGF
HRRARASDRS NATQLDGPAG ALLLRLVQLA GAPEPFEPAQ PDAY*
speed 0.46 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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