Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000311813
Querying Taster for transcript #2: ENST00000434909
MT speed 2.33 s - this script 6.308256 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AQP1disease_causing_automatic0.99966473481943simple_aae0P98Lsingle base exchangers104894004show file
AQP1disease_causing_automatic0.999909090244902simple_aae0P38Lsingle base exchangers104894004show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99966473481943 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940080)
  • known disease mutation: rs17847 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:30951637C>TN/A show variant in all transcripts   IGV
HGNC symbol AQP1
Ensembl transcript ID ENST00000434909
Genbank transcript ID N/A
UniProt peptide P29972
alteration type single base exchange
alteration region CDS
DNA changes c.293C>T
cDNA.644C>T
g.58628C>T
AA changes P98L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
98
frameshift no
known variant Reference ID: rs104894004
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs17847 (pathogenic for Colton-null phenotype) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2380.998
1.8070.937
(flanking)-1.2280.027
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 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      98TNIGSALGFKYPVGNNQTAVQDNV
mutated  not conserved    98TNIGSALGFKYLVGNNQTAVQDN
Ptroglodytes  all identical  ENSPTRG00000019047  38ISIGSALGFKYPVGNNQTAVQDN
Mmulatta  all identical  ENSMMUG00000011763  38ISIGSALGFKYPVGNNQTVVQDN
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  all identical  ENSGALG00000005209  38ISIGSALGFNFPVSVNGTSATQDN
Trubripes  not conserved  ENSTRUG00000013591  38LSISTAIGNK----NNSNPDQE-
Drerio  no alignment  ENSDARG00000023713  n/a
Dmelanogaster  not conserved  FBgn0015872  36MLLGELVGTFFLIFVGVGSTTSGSV
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
94114HELIXlost
95115TRANSMEMHelical; Name=Helix 3.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1341 / 1341
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 352 / 352
chromosome 7
strand 1
last intron/exon boundary 1162
theoretical NMD boundary in CDS 760
length of CDS 990
coding sequence (CDS) position 293
cDNA position
(for ins/del: last normal base / first normal base)
644
gDNA position
(for ins/del: last normal base / first normal base)
58628
chromosomal position
(for ins/del: last normal base / first normal base)
30951637
original gDNA sequence snippet TGCCCTGGGCTTCAAATACCCGGTGGGGAACAACCAGACGG
altered gDNA sequence snippet TGCCCTGGGCTTCAAATACCTGGTGGGGAACAACCAGACGG
original cDNA sequence snippet TGCCCTGGGCTTCAAATACCCGGTGGGGAACAACCAGACGG
altered cDNA sequence snippet TGCCCTGGGCTTCAAATACCTGGTGGGGAACAACCAGACGG
wildtype AA sequence MCQVGCFLKT PRFPIWVVCS ESHFSILFSL QPGLLRDWRT ERLFDLYYYD GLANQQEQIR
LTIDTTQTIS EDTDNDLVPP LELCIRTNIG SALGFKYPVG NNQTAVQDNV KVSLAFGLSI
ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
RVKVWTSGQV EEYDLDADDI NSRVEMKPK*
mutated AA sequence MCQVGCFLKT PRFPIWVVCS ESHFSILFSL QPGLLRDWRT ERLFDLYYYD GLANQQEQIR
LTIDTTQTIS EDTDNDLVPP LELCIRTNIG SALGFKYLVG NNQTAVQDNV KVSLAFGLSI
ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
RVKVWTSGQV EEYDLDADDI NSRVEMKPK*
speed 1.34 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999909090244902 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940080)
  • known disease mutation: rs17847 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:30951637C>TN/A show variant in all transcripts   IGV
HGNC symbol AQP1
Ensembl transcript ID ENST00000311813
Genbank transcript ID NM_198098
UniProt peptide P29972
alteration type single base exchange
alteration region CDS
DNA changes c.113C>T
cDNA.168C>T
g.58628C>T
AA changes P38L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
38
frameshift no
known variant Reference ID: rs104894004
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC055

known disease mutation: rs17847 (pathogenic for Colton-null phenotype) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940080)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2380.998
1.8070.937
(flanking)-1.2280.027
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 168
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      38ISIGSALGFKYPVGNNQTAVQDNV
mutated  not conserved    38ISIGSALGFKYLVGNNQTAVQDN
Ptroglodytes  all identical  ENSPTRG00000019047  38ISIGSALGFKYPVGNNQTAVQDN
Mmulatta  all identical  ENSMMUG00000011763  38ISIGSALGFKYPVGNNQTVVQDN
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  all identical  ENSGALG00000005209  38ISIGSALGFNFPVSVNGTSATQDN
Trubripes  not conserved  ENSTRUG00000013591  38LSISTAIGNK----NNSNPDQE-
Drerio  not conserved  ENSDARG00000023713  37LSITAA------VGNTNTQNPDQE
Dmelanogaster  all identical  FBgn0015872  50VGVGSTTSGSVP-----------
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
3742STRANDlost
3748TOPO_DOMExtracellular.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 810 / 810
position (AA) of stopcodon in wt / mu AA sequence 270 / 270
position of stopcodon in wt / mu cDNA 865 / 865
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 56 / 56
chromosome 7
strand 1
last intron/exon boundary 686
theoretical NMD boundary in CDS 580
length of CDS 810
coding sequence (CDS) position 113
cDNA position
(for ins/del: last normal base / first normal base)
168
gDNA position
(for ins/del: last normal base / first normal base)
58628
chromosomal position
(for ins/del: last normal base / first normal base)
30951637
original gDNA sequence snippet TGCCCTGGGCTTCAAATACCCGGTGGGGAACAACCAGACGG
altered gDNA sequence snippet TGCCCTGGGCTTCAAATACCTGGTGGGGAACAACCAGACGG
original cDNA sequence snippet TGCCCTGGGCTTCAAATACCCGGTGGGGAACAACCAGACGG
altered cDNA sequence snippet TGCCCTGGGCTTCAAATACCTGGTGGGGAACAACCAGACGG
wildtype AA sequence MASEFKKKLF WRAVVAEFLA TTLFVFISIG SALGFKYPVG NNQTAVQDNV KVSLAFGLSI
ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
RVKVWTSGQV EEYDLDADDI NSRVEMKPK*
mutated AA sequence MASEFKKKLF WRAVVAEFLA TTLFVFISIG SALGFKYLVG NNQTAVQDNV KVSLAFGLSI
ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
RVKVWTSGQV EEYDLDADDI NSRVEMKPK*
speed 0.99 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
back to results table

Problems