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: ENST00000229335
Querying Taster for transcript #2: ENST00000537228
MT speed 3.25 s - this script 5.282157 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AICDAdisease_causing_automatic0.999999474398142simple_aaeaffected0R24Wsingle base exchangers104894324show file
AICDAdisease_causing_automatic0.999999474398142simple_aaeaffected0R24Wsingle base exchangers104894324show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999474398142 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002421)
  • known disease mutation: rs5122 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:8759547G>AN/A show variant in all transcripts   IGV
HGNC symbol AICDA
Ensembl transcript ID ENST00000229335
Genbank transcript ID NM_020661
UniProt peptide Q9GZX7
alteration type single base exchange
alteration region CDS
DNA changes c.70C>T
cDNA.174C>T
g.5921C>T
AA changes R24W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
24
frameshift no
known variant Reference ID: rs104894324
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5122 (pathogenic for Hyper-IgM syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2710.986
1.7320.963
(flanking)-1.0550.595
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5926wt: 0.59 / mu: 0.66wt: CGGCGTGAGACCTAC
mu: TGGCGTGAGACCTAC
 GCGT|gaga
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      24YQFKNVRWAKGRRETYLCYVVKRR
mutated  not conserved    24YQFKNVRWAKGWRETYLCYVVKR
Ptroglodytes  all identical  ENSPTRG00000004640  24YQFKNVRWAKGRRETYLCYVVKR
Mmulatta  all identical  ENSMMUG00000019134  23YHFKNVRWAKGRHETYLCYVVKR
Fcatus  no alignment  ENSFCAG00000006052  n/a
Mmusculus  all identical  ENSMUSG00000040627  24YHFKNVRWAKGRHETYLCYVVKR
Ggallus  all identical  ENSGALG00000014280  24YNFKNLRWAKGRRETYLCYVVKR
Trubripes  all identical  ENSTRUG00000007079  28YHYKNVRWARGRHETYLCFVVKR
Drerio  all identical  ENSDARG00000015734  28FHYKNVRWARGRHETYLCFVVKR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023905  26YHYKNLRWARGRHETYLCYIVKR
protein features
start (aa)end (aa)featuredetails 
130REGIONNuclear localization signal.lost
3838MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
3838MUTAGENS->A,D: No effect on interaction with CTNNBL1.might get lost (downstream of altered splice site)
3942MUTAGENATSF->GGQV: Greatly reduced interaction with CTNNBL1 but no effect on subcellular location, enzyme activity, ability to oligomerize nor on phosphorylation at Ser-38. Diminished antibody diversification.might get lost (downstream of altered splice site)
3942REGIONImportant for interaction with CTNNBL1.might get lost (downstream of altered splice site)
5050MUTAGENR->G: Some reduced nuclear import; when associated with A-193.might get lost (downstream of altered splice site)
5656METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
5858ACT_SITEProton donor (By similarity).might get lost (downstream of altered splice site)
8787METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
9090METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
112112MUTAGENR->D: Greatly reduced nuclear import; when associated with A-193.might get lost (downstream of altered splice site)
183198REGIONNuclear export signal.might get lost (downstream of altered splice site)
193193MUTAGENF->A: Completely abolishes nuclear import; when associated with W-24 or D- 112. Little affect on nuclear import; when associated with A-10. Greatly impaired nuclear import; when associated with K-20 or G-50. Almost completely abolishes nuclear import; when associated with S-18 and V-19.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 597 / 597
position (AA) of stopcodon in wt / mu AA sequence 199 / 199
position of stopcodon in wt / mu cDNA 701 / 701
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 105 / 105
chromosome 12
strand -1
last intron/exon boundary 648
theoretical NMD boundary in CDS 493
length of CDS 597
coding sequence (CDS) position 70
cDNA position
(for ins/del: last normal base / first normal base)
174
gDNA position
(for ins/del: last normal base / first normal base)
5921
chromosomal position
(for ins/del: last normal base / first normal base)
8759547
original gDNA sequence snippet ATGTCCGCTGGGCTAAGGGTCGGCGTGAGACCTACCTGTGC
altered gDNA sequence snippet ATGTCCGCTGGGCTAAGGGTTGGCGTGAGACCTACCTGTGC
original cDNA sequence snippet ATGTCCGCTGGGCTAAGGGTCGGCGTGAGACCTACCTGTGC
altered cDNA sequence snippet ATGTCCGCTGGGCTAAGGGTTGGCGTGAGACCTACCTGTGC
wildtype AA sequence MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*
mutated AA sequence MDSLLMNRRK FLYQFKNVRW AKGWRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*
speed 1.77 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: 0.999999474398142 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002421)
  • known disease mutation: rs5122 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:8759547G>AN/A show variant in all transcripts   IGV
HGNC symbol AICDA
Ensembl transcript ID ENST00000537228
Genbank transcript ID N/A
UniProt peptide Q9GZX7
alteration type single base exchange
alteration region CDS
DNA changes c.70C>T
cDNA.170C>T
g.5921C>T
AA changes R24W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
24
frameshift no
known variant Reference ID: rs104894324
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5122 (pathogenic for Hyper-IgM syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002421)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2710.986
1.7320.963
(flanking)-1.0550.595
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased5926wt: 0.59 / mu: 0.66wt: CGGCGTGAGACCTAC
mu: TGGCGTGAGACCTAC
 GCGT|gaga
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      24YQFKNVRWAKGRRETYLCYVVKRR
mutated  not conserved    24YQFKNVRWAKGWRETYLCYVVKR
Ptroglodytes  all identical  ENSPTRG00000004640  24YQFKNVRWAKGRRETYLCYVVKR
Mmulatta  all identical  ENSMMUG00000019134  23YHFKNVRWAKGRHETYLCYVVKR
Fcatus  no alignment  ENSFCAG00000006052  n/a
Mmusculus  all identical  ENSMUSG00000040627  24YHFKNVRWAKGRHETYLCYVVKR
Ggallus  all identical  ENSGALG00000014280  24YNFKNLRWAKGRRETYLCYVVKR
Trubripes  all identical  ENSTRUG00000007079  28YHYKNVRWARGRHETYLCFVVKR
Drerio  all identical  ENSDARG00000015734  28FHYKNVRWARGRHETYLCFVVKR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023905  26YHYKNLRWARGRHETYLCYIVKR
protein features
start (aa)end (aa)featuredetails 
130REGIONNuclear localization signal.lost
3838MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
3838MUTAGENS->A,D: No effect on interaction with CTNNBL1.might get lost (downstream of altered splice site)
3942MUTAGENATSF->GGQV: Greatly reduced interaction with CTNNBL1 but no effect on subcellular location, enzyme activity, ability to oligomerize nor on phosphorylation at Ser-38. Diminished antibody diversification.might get lost (downstream of altered splice site)
3942REGIONImportant for interaction with CTNNBL1.might get lost (downstream of altered splice site)
5050MUTAGENR->G: Some reduced nuclear import; when associated with A-193.might get lost (downstream of altered splice site)
5656METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
5858ACT_SITEProton donor (By similarity).might get lost (downstream of altered splice site)
8787METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
9090METALZinc; catalytic (By similarity).might get lost (downstream of altered splice site)
112112MUTAGENR->D: Greatly reduced nuclear import; when associated with A-193.might get lost (downstream of altered splice site)
183198REGIONNuclear export signal.might get lost (downstream of altered splice site)
193193MUTAGENF->A: Completely abolishes nuclear import; when associated with W-24 or D- 112. Little affect on nuclear import; when associated with A-10. Greatly impaired nuclear import; when associated with K-20 or G-50. Almost completely abolishes nuclear import; when associated with S-18 and V-19.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 567 / 567
position (AA) of stopcodon in wt / mu AA sequence 189 / 189
position of stopcodon in wt / mu cDNA 667 / 667
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 101 / 101
chromosome 12
strand -1
last intron/exon boundary 614
theoretical NMD boundary in CDS 463
length of CDS 567
coding sequence (CDS) position 70
cDNA position
(for ins/del: last normal base / first normal base)
170
gDNA position
(for ins/del: last normal base / first normal base)
5921
chromosomal position
(for ins/del: last normal base / first normal base)
8759547
original gDNA sequence snippet ATGTCCGCTGGGCTAAGGGTCGGCGTGAGACCTACCTGTGC
altered gDNA sequence snippet ATGTCCGCTGGGCTAAGGGTTGGCGTGAGACCTACCTGTGC
original cDNA sequence snippet ATGTCCGCTGGGCTAAGGGTCGGCGTGAGACCTACCTGTGC
altered cDNA sequence snippet ATGTCCGCTGGGCTAAGGGTTGGCGTGAGACCTACCTGTGC
wildtype AA sequence MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR
DAFRTLGL*
mutated AA sequence MDSLLMNRRK FLYQFKNVRW AKGWRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR
DAFRTLGL*
speed 1.48 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