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 0 s - this script 4.062419 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AICDAdisease_causing_automatic0.999999995626279simple_aae0W80Rsingle base exchangers104894320show file
AICDAdisease_causing_automatic0.999999995626279simple_aae0W80Rsingle base exchangers104894320show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995626279 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002423)
  • known disease mutation: rs5124 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:8758000A>GN/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.238T>C
cDNA.342T>C
g.7468T>C
AA changes W80R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 80
frameshift no
known variant Reference ID: rs104894320
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5124 (pathogenic for Hyper-IgM syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3111
4.4011
(flanking)0.7351
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 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      80DLDPGRCYRVTWFTSWSPCYDCAR
mutated  not conserved    80DLDPGRCYRVTRFTSWSPCYDCA
Ptroglodytes  all identical  ENSPTRG00000004640  80DLDPGRCYRVTWFTSWSPCYDCA
Mmulatta  all identical  ENSMMUG00000019134  79DLDPGRCYRVTWFTSWSPCYDCA
Fcatus  all identical  ENSFCAG00000006052  28DLDPGRCYRVTWFTSWSPCYDCA
Mmusculus  all identical  ENSMUSG00000040627  80DLDPGRCYRVTWFTSWSPCYDCA
Ggallus  all identical  ENSGALG00000014280  80DLDPGRCYRITWFTSWSPCYDCA
Trubripes  all identical  ENSTRUG00000007079  84ALCPGLWGYGAAGEKRLSYSVTWFCSWSPCVNCS
Drerio  all identical  ENSDARG00000015734  84SVDGARLCYSVTWFCSWSPCSKCA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023905  82GHDPHRAYRVTWFSSWSPCYDCA
protein features no protein features affected
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 238
cDNA position
(for ins/del: last normal base / first normal base)		 342
gDNA position
(for ins/del: last normal base / first normal base)		 7468
chromosomal position
(for ins/del: last normal base / first normal base)		 8758000
original gDNA sequence snippet GCCGCTGCTACCGCGTCACCTGGTTCACCTCCTGGAGCCCC
altered gDNA sequence snippet GCCGCTGCTACCGCGTCACCCGGTTCACCTCCTGGAGCCCC
original cDNA sequence snippet GCCGCTGCTACCGCGTCACCTGGTTCACCTCCTGGAGCCCC
altered cDNA sequence snippet GCCGCTGCTACCGCGTCACCCGGTTCACCTCCTGGAGCCCC
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 AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTR FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL
LPLYEVDDLR DAFRTLGL*
speed 0.70 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: 0.999999995626279 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002423)
  • known disease mutation: rs5124 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:8758000A>GN/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.238T>C
cDNA.338T>C
g.7468T>C
AA changes W80R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 80
frameshift no
known variant Reference ID: rs104894320
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5124 (pathogenic for Hyper-IgM syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002423)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3111
4.4011
(flanking)0.7351
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 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      80DLDPGRCYRVTWFTSWSPCYDCAR
mutated  not conserved    80DLDPGRCYRVTRFTSWSPCYDCA
Ptroglodytes  all identical  ENSPTRG00000004640  80DLDPGRCYRVTWFTSWSPCYDCA
Mmulatta  all identical  ENSMMUG00000019134  79DLDPGRCYRVTWFTSWSPCYDCA
Fcatus  all identical  ENSFCAG00000006052  28DLDPGRCYRVTWFTSWSPCYDCA
Mmusculus  all identical  ENSMUSG00000040627  80DLDPGRCYRVTWFTSWSPCYDCA
Ggallus  all identical  ENSGALG00000014280  80DLDPGRCYRITWFTSWSPCYDCA
Trubripes  all identical  ENSTRUG00000007079  84ALCPGLWGYGAAGEKRLSYSVTWFCSWSPCVNCS
Drerio  all identical  ENSDARG00000015734  84SVDGARLCYSVTWFCSWSPCSKCA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023905  82GHDPHRAYRVTWFSSWSPCYDCA
protein features no protein features affected
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 238
cDNA position
(for ins/del: last normal base / first normal base)		 338
gDNA position
(for ins/del: last normal base / first normal base)		 7468
chromosomal position
(for ins/del: last normal base / first normal base)		 8758000
original gDNA sequence snippet GCCGCTGCTACCGCGTCACCTGGTTCACCTCCTGGAGCCCC
altered gDNA sequence snippet GCCGCTGCTACCGCGTCACCCGGTTCACCTCCTGGAGCCCC
original cDNA sequence snippet GCCGCTGCTACCGCGTCACCTGGTTCACCTCCTGGAGCCCC
altered cDNA sequence snippet GCCGCTGCTACCGCGTCACCCGGTTCACCTCCTGGAGCCCC
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 AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL
FLRYISDWDL DPGRCYRVTR FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK
AEPEGLRRLH RAGVQIAIMT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR
DAFRTLGL*
speed 0.68 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

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