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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: ENST00000199280
MT speed 0 s - this script 2.830928 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AQP2disease_causing_automatic0.999871357163392simple_aae0P262Lsingle base exchangers104894339show file

Taster files

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Prediction

disease causing

 Model: simple_aae, prob: 0.999871357163392 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950083)
  • known disease mutation: rs17844 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:50349360C>TN/A show variant in all transcripts   IGV
HGNC symbol AQP2
Ensembl transcript ID ENST00000199280
Genbank transcript ID NM_000486
UniProt peptide P41181
alteration type single base exchange
alteration region CDS
DNA changes c.785C>T
cDNA.870C>T
g.4837C>T
AA changes P262L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 262
frameshift no
known variant Reference ID: rs104894339
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC077

known disease mutation: rs17844 (pathogenic for Diabetes insipidus, nephrogenic, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950083)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0931
3.8331
(flanking)0.7861
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 179
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      262VRRRQSVELHSPQSLPRGTKA*
mutated  not conserved    262VRRRQSVELHSLQSLPRGTKA
Ptroglodytes  all identical  ENSPTRG00000004918  241VRRRQSVELHSPQSLPRGTKA
Mmulatta  all identical  ENSMMUG00000022916  262VRRRQSVELHSPQSLPRGTKA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000023013  262VRRRQSVELHSPQSLPRGSKA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0015872  n/a
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020388  263EQKRQSVELYSAHPLPK
protein features
start (aa)end (aa)featuredetails 
225271TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 816 / 816
position (AA) of stopcodon in wt / mu AA sequence 272 / 272
position of stopcodon in wt / mu cDNA 901 / 901
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 86 / 86
chromosome 12
strand 1
last intron/exon boundary 692
theoretical NMD boundary in CDS 556
length of CDS 816
coding sequence (CDS) position 785
cDNA position
(for ins/del: last normal base / first normal base)		 870
gDNA position
(for ins/del: last normal base / first normal base)		 4837
chromosomal position
(for ins/del: last normal base / first normal base)		 50349360
original gDNA sequence snippet GTCGGTGGAGCTGCACTCGCCGCAGAGCCTGCCACGGGGTA
altered gDNA sequence snippet GTCGGTGGAGCTGCACTCGCTGCAGAGCCTGCCACGGGGTA
original cDNA sequence snippet GTCGGTGGAGCTGCACTCGCCGCAGAGCCTGCCACGGGGTA
altered cDNA sequence snippet GTCGGTGGAGCTGCACTCGCTGCAGAGCCTGCCACGGGGTA
wildtype AA sequence MWELRSIAFS RAVFAEFLAT LLFVFFGLGS ALNWPQALPS VLQIAMAFGL GIGTLVQALG
HISGAHINPA VTVACLVGCH VSVLRAAFYV AAQLLGAVAG AALLHEITPA DIRGDLAVNA
LSNSTTAGQA VTVELFLTLQ LVLCIFASTD ERRGENPGTP ALSIGFSVAL GHLLGIHYTG
CSMNPARSLA PAVVTGKFDD HWVFWIGPLV GAILGSLLYN YVLFPPAKSL SERLAVLKGL
EPDTDWEERE VRRRQSVELH SPQSLPRGTK A*
mutated AA sequence MWELRSIAFS RAVFAEFLAT LLFVFFGLGS ALNWPQALPS VLQIAMAFGL GIGTLVQALG
HISGAHINPA VTVACLVGCH VSVLRAAFYV AAQLLGAVAG AALLHEITPA DIRGDLAVNA
LSNSTTAGQA VTVELFLTLQ LVLCIFASTD ERRGENPGTP ALSIGFSVAL GHLLGIHYTG
CSMNPARSLA PAVVTGKFDD HWVFWIGPLV GAILGSLLYN YVLFPPAKSL SERLAVLKGL
EPDTDWEERE VRRRQSVELH SLQSLPRGTK A*
speed 0.82 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