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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 1.2 s - this script 5.36716 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AVPdisease_causing_automatic0.999924741757428simple_aaeaffected0Y21Hsingle base exchangers121964893show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999924741757428 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM962570)
  • known disease mutation: rs12221 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:3065260A>GN/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.61T>C
cDNA.111T>C
g.111T>C
AA changes Y21H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS
21
frameshift no
known variant Reference ID: rs121964893
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs12221 (pathogenic for Neurohypophyseal diabetes insipidus) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM962570)

known disease mutation at this position, please check HGMD for details (HGMD ID CM962570)
known disease mutation at this position, please check HGMD for details (HGMD ID CM962570)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0151
5.0151
(flanking)1.7891
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 increased112wt: 0.3060 / mu: 0.3334 (marginal change - not scored)wt: GGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGCCCGAGGG
mu: GGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGCCCGAGGG
 gcta|CTTC
Acc marginally increased105wt: 0.9527 / mu: 0.9671 (marginal change - not scored)wt: GCCTACTGGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGC
mu: GCCTACTGGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGC
 tccg|CGTG
Acc marginally increased118wt: 0.9124 / mu: 0.9166 (marginal change - not scored)wt: CTCCTCCGCGTGCTACTTCCAGAACTGCCCGAGGGGCGGCA
mu: CTCCTCCGCGTGCCACTTCCAGAACTGCCCGAGGGGCGGCA
 tcca|GAAC
Acc increased103wt: 0.44 / mu: 0.52wt: CGGCCTACTGGCCTTCTCCTCCGCGTGCTACTTCCAGAACT
mu: CGGCCTACTGGCCTTCTCCTCCGCGTGCCACTTCCAGAACT
 cctc|CGCG
Acc marginally increased106wt: 0.9182 / mu: 0.9479 (marginal change - not scored)wt: CCTACTGGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGCC
mu: CCTACTGGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGCC
 ccgc|GTGC
Acc marginally increased108wt: 0.9703 / mu: 0.9756 (marginal change - not scored)wt: TACTGGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGCCCG
mu: TACTGGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGCCCG
 gcgt|GCTA
Donor increased116wt: 0.49 / mu: 0.67wt: TACTTCCAGAACTGC
mu: CACTTCCAGAACTGC
 CTTC|caga
Donor increased108wt: 0.36 / mu: 0.62wt: CCGCGTGCTACTTCC
mu: CCGCGTGCCACTTCC
 GCGT|gcta
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      21FLGLLAFSSACYFQNCPRGGKRAM
mutated  all conserved    21FLGLLAFSSACHFQNCPRGGKRA
Ptroglodytes  all identical  ENSPTRG00000013190  21FLGLVALSSGWYFQNCPRGGKRA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000037727  25FLSLLAFSSACYFQNCPRGGKRA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000058567  23VLCVLALSTLSSACYIQNCPRGGKRS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
119SIGNALmight get lost (downstream of altered splice site)
2020DISULFIDmight get lost (downstream of altered splice site)
2028PEPTIDEArg-vasopressin. /FTId=PRO_0000020515.lost
2525DISULFIDmight get lost (downstream of altered splice site)
2828MOD_RESGlycine amide.might get lost (downstream of altered splice site)
4141DISULFIDBy similarity.might get lost (downstream of altered splice site)
4444DISULFIDBy similarity.might get lost (downstream of altered splice site)
4848CONFLICTG -> D (in Ref. 5; AAB86629).might get lost (downstream of altered splice site)
5252DISULFIDBy similarity.might get lost (downstream of altered splice site)
5858DISULFIDBy similarity.might get lost (downstream of altered splice site)
5959DISULFIDBy similarity.might get lost (downstream of altered splice site)
6565DISULFIDBy similarity.might get lost (downstream of altered splice site)
7575DISULFIDBy similarity.might get lost (downstream of altered splice site)
8585DISULFIDBy similarity.might get lost (downstream of altered splice site)
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 61
cDNA position
(for ins/del: last normal base / first normal base)
111
gDNA position
(for ins/del: last normal base / first normal base)
111
chromosomal position
(for ins/del: last normal base / first normal base)
3065260
original gDNA sequence snippet TGGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGCCCGAGG
altered gDNA sequence snippet TGGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGCCCGAGG
original cDNA sequence snippet TGGCCTTCTCCTCCGCGTGCTACTTCCAGAACTGCCCGAGG
altered cDNA sequence snippet TGGCCTTCTCCTCCGCGTGCCACTTCCAGAACTGCCCGAGG
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 HFQNCPRGGK RAMSDLELRQ CLPCGPGGKG RCFGPSICCA
DELGCFVGTA EALRCQEENY LPSPCQSGQK ACGSGGRCAA FGVCCNDESC VTEPECREGF
HRRARASDRS NATQLDGPAG ALLLRLVQLA GAPEPFEPAQ PDAY*
speed 1.20 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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