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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 0.88 s - this script 2.975163 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AQP2disease_causing_automatic0.999673291460445simple_aaeaffected0G175Rsingle base exchangers104894335show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999673291460445 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980101)
  • known disease mutation: rs17835 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:50348100G>AN/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.523G>A
cDNA.608G>A
g.3577G>A
AA changes G175R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 175
frameshift no
known variant Reference ID: rs104894335
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17835 (pathogenic for Diabetes insipidus, nephrogenic, autosomal recessive) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980101)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980101)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980101)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.5450.335
3.6020.998
(flanking)2.4931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost3578sequence motif lost- wt: TGGG|gtag
 mu: TAGG.gtag
Acc marginally increased3577wt: 0.5758 / mu: 0.6209 (marginal change - not scored)wt: TGGCCCTGGGCCACCTCCTTGGGGTAGGTCATGGCCATGGG
mu: TGGCCCTGGGCCACCTCCTTAGGGTAGGTCATGGCCATGGG		 cttg|GGGT
Acc marginally decreased3578wt: 0.7682 / mu: 0.7555 (marginal change - not scored)wt: GGCCCTGGGCCACCTCCTTGGGGTAGGTCATGGCCATGGGT
mu: GGCCCTGGGCCACCTCCTTAGGGTAGGTCATGGCCATGGGT		 ttgg|GGTA
Donor increased3577wt: 0.20 / mu: 0.89wt: TCCTTGGGGTAGGTC
mu: TCCTTAGGGTAGGTC		 CTTG|gggt
Acc gained35790.37mu: GCCCTGGGCCACCTCCTTAGGGTAGGTCATGGCCATGGGTT tagg|GTAG
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      175IGFSVALGHLLGIHYTGCSMNPAR
mutated  not conserved    175IGFSVALGHLLRIHYTG
Ptroglodytes  all identical  ENSPTRG00000004918  175IGFSVALGHLLG-----
Mmulatta  all identical  ENSMMUG00000022916  175IGFSVALGHLLGIHYTG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000023013  175IGFSVTLGHLLGIYFTG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0015872  183VGLAIAAGHLCAIKLSGASMNPA
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020388  176IGLSVTVGHLLGIYLTGCS
protein features
start (aa)end (aa)featuredetails 
157176TRANSMEMHelical; (Potential).lost
177202TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
184186MOTIFNPA 2.might get lost (downstream of altered splice site)
203224TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
225271TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
229229MUTAGENS->A: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
229229MUTAGENS->D: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
231231MUTAGENS->A: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
231231MUTAGENS->D: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
244244MUTAGENT->E: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
244244MUTAGENT->A: No effect on sorting from the ER to the vesicles, redistribution to apical membrane, or endocytosis.might get lost (downstream of altered splice site)
256256MUTAGENS->D: Expressed in the apical membrane.might get lost (downstream of altered splice site)
256256MUTAGENS->A: Retained in vesicles.might get lost (downstream of altered splice site)
256256MOD_RESPhosphoserine; by PKA.might get lost (downstream of altered splice site)
261261MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
264264MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
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 523
cDNA position
(for ins/del: last normal base / first normal base)		 608
gDNA position
(for ins/del: last normal base / first normal base)		 3577
chromosomal position
(for ins/del: last normal base / first normal base)		 50348100
original gDNA sequence snippet TGGCCCTGGGCCACCTCCTTGGGGTAGGTCATGGCCATGGG
altered gDNA sequence snippet TGGCCCTGGGCCACCTCCTTAGGGTAGGTCATGGCCATGGG
original cDNA sequence snippet TGGCCCTGGGCCACCTCCTTGGGATCCATTACACCGGCTGC
altered cDNA sequence snippet TGGCCCTGGGCCACCTCCTTAGGATCCATTACACCGGCTGC
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 GHLLRIHYTG
CSMNPARSLA PAVVTGKFDD HWVFWIGPLV GAILGSLLYN YVLFPPAKSL SERLAVLKGL
EPDTDWEERE VRRRQSVELH SPQSLPRGTK A*
speed 0.88 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