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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 1.4 s - this script 6.982522 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AQP2disease_causing_automatic0.999999383732835simple_aaeaffected0A147Tsingle base exchangers104894334show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999999383732835 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970101)
  • known disease mutation: rs17832 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:50348016G>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.439G>A
cDNA.524G>A
g.3493G>A
AA changes A147T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
147
frameshift no
known variant Reference ID: rs104894334
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC088

known disease mutation: rs17832 (pathogenic for Nephrogenic diabetes insipidus|Diabetes insipidus, nephrogenic, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970101)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970101)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970101)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3210.965
5.2421
(flanking)5.2421
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 increased3497wt: 0.2572 / mu: 0.2637 (marginal change - not scored)wt: GGTGCTCTGCATCTTCGCCTCCACCGATGAGCGCCGCGGAG
mu: GGTGCTCTGCATCTTCACCTCCACCGATGAGCGCCGCGGAG
 cctc|CACC
Acc increased3496wt: 0.46 / mu: 0.57wt: TGGTGCTCTGCATCTTCGCCTCCACCGATGAGCGCCGCGGA
mu: TGGTGCTCTGCATCTTCACCTCCACCGATGAGCGCCGCGGA
 gcct|CCAC
Acc marginally increased3494wt: 0.5338 / mu: 0.5568 (marginal change - not scored)wt: GCTGGTGCTCTGCATCTTCGCCTCCACCGATGAGCGCCGCG
mu: GCTGGTGCTCTGCATCTTCACCTCCACCGATGAGCGCCGCG
 tcgc|CTCC
distance from splice site 79
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      147FLTLQLVLCIFASTDERRGENPGT
mutated  not conserved    147FLTLQLVLCIFTSTDERRGENPG
Ptroglodytes  all identical  ENSPTRG00000004918  147FLTLQLVLCIFASTDERRGENPG
Mmulatta  all identical  ENSMMUG00000022916  147FLTLQLVLCIFASTDERRGENPG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000023013  147FLTMQLVLCIFASTDERRSDNLG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0015872  155LITFILVFVVKAVSDPGRQDIKG
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020388  148FLTFQLVLCVFASTDSRRSDNVG
protein features
start (aa)end (aa)featuredetails 
128148TRANSMEMHelical; (Potential).lost
148148MUTAGENS->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)
148148MUTAGENS->D: Retained in the endoplasmic reticulum.might get lost (downstream of altered splice site)
149156TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
157176TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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->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->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)
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 439
cDNA position
(for ins/del: last normal base / first normal base)
524
gDNA position
(for ins/del: last normal base / first normal base)
3493
chromosomal position
(for ins/del: last normal base / first normal base)
50348016
original gDNA sequence snippet AGCTGGTGCTCTGCATCTTCGCCTCCACCGATGAGCGCCGC
altered gDNA sequence snippet AGCTGGTGCTCTGCATCTTCACCTCCACCGATGAGCGCCGC
original cDNA sequence snippet AGCTGGTGCTCTGCATCTTCGCCTCCACCGATGAGCGCCGC
altered cDNA sequence snippet AGCTGGTGCTCTGCATCTTCACCTCCACCGATGAGCGCCGC
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 LVLCIFTSTD ERRGENPGTP ALSIGFSVAL GHLLGIHYTG
CSMNPARSLA PAVVTGKFDD HWVFWIGPLV GAILGSLLYN YVLFPPAKSL SERLAVLKGL
EPDTDWEERE VRRRQSVELH SPQSLPRGTK A*
speed 1.40 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