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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 2.941542 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AQP2disease_causing_automatic0.361723583967077simple_aaeaffected0A190Tsingle base exchangers104894341show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.361723583967077 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950082)
  • known disease mutation: rs17845 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:50348455G>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.568G>A
cDNA.653G>A
g.3932G>A
AA changes A190T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 190
frameshift no
known variant Reference ID: rs104894341
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17845 (pathogenic for Diabetes insipidus, nephrogenic, autosomal recessive) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950082)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950082)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3691
3.8711
(flanking)2.6211
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 increased3930wt: 0.8564 / mu: 0.8612 (marginal change - not scored)wt: TATGAATCCTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTG
mu: TATGAATCCTGCCCGCTCCCTGACTCCAGCTGTCGTCACTG		 ccct|GGCT
Acc marginally increased3938wt: 0.3603 / mu: 0.4379 (marginal change - not scored)wt: CTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTGGCAAATTT
mu: CTGCCCGCTCCCTGACTCCAGCTGTCGTCACTGGCAAATTT		 ccag|CTGT
Acc increased3937wt: 0.54 / mu: 0.62wt: CCTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTGGCAAATT
mu: CCTGCCCGCTCCCTGACTCCAGCTGTCGTCACTGGCAAATT		 tcca|GCTG
Acc marginally increased3927wt: 0.4515 / mu: 0.4919 (marginal change - not scored)wt: CTCTATGAATCCTGCCCGCTCCCTGGCTCCAGCTGTCGTCA
mu: CTCTATGAATCCTGCCCGCTCCCTGACTCCAGCTGTCGTCA		 gctc|CCTG
Acc marginally increased3932wt: 0.8456 / mu: 0.8695 (marginal change - not scored)wt: TGAATCCTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTGGC
mu: TGAATCCTGCCCGCTCCCTGACTCCAGCTGTCGTCACTGGC		 ctgg|CTCC
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      190TGCSMNPARSLAPAVVTGKFDDHW
mutated  not conserved    190CSMNPARSLTPAVVTGKFDDH
Ptroglodytes  not conserved  ENSPTRG00000004918  185--------------TGK-DDH
Mmulatta  all identical  ENSMMUG00000022916  190CSMNPARSLAPAVVTGKFDDH
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000023013  190CSMNPARSLAPAVVTGKFDDH
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0015872  198SGASMNPARSFGPAVVQGVWTYH
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020388  190MNPARSFGPAAITGIFTDH
protein features
start (aa)end (aa)featuredetails 
177202TOPO_DOMExtracellular (Potential).lost
203224TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
225271TOPO_DOMCytoplasmic (Potential).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)
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)
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)
256256MOD_RESPhosphoserine; by PKA.might get lost (downstream of altered splice site)
256256MUTAGENS->A: Retained in vesicles.might get lost (downstream of altered splice site)
256256MUTAGENS->D: Expressed in the apical membrane.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 568
cDNA position
(for ins/del: last normal base / first normal base)		 653
gDNA position
(for ins/del: last normal base / first normal base)		 3932
chromosomal position
(for ins/del: last normal base / first normal base)		 50348455
original gDNA sequence snippet TGAATCCTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTGGC
altered gDNA sequence snippet TGAATCCTGCCCGCTCCCTGACTCCAGCTGTCGTCACTGGC
original cDNA sequence snippet TGAATCCTGCCCGCTCCCTGGCTCCAGCTGTCGTCACTGGC
altered cDNA sequence snippet TGAATCCTGCCCGCTCCCTGACTCCAGCTGTCGTCACTGGC
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
CSMNPARSLT PAVVTGKFDD HWVFWIGPLV GAILGSLLYN YVLFPPAKSL SERLAVLKGL
EPDTDWEERE VRRRQSVELH SPQSLPRGTK A*
speed 0.83 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