Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000375326
Querying Taster for transcript #2: ENST00000415431
MT speed 0 s - this script 3.746824 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FBP1disease_causing_automatic0.999999999735923simple_aaeaffected0G164Ssingle base exchangers121918188show file
FBP1disease_causing_automatic0.999999999735923simple_aaeaffected0G164Ssingle base exchangers121918188show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999735923 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970524)
  • known disease mutation: rs868 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:97372280C>TN/A show variant in all transcripts   IGV
HGNC symbol FBP1
Ensembl transcript ID ENST00000375326
Genbank transcript ID NM_000507
UniProt peptide P09467
alteration type single base exchange
alteration region CDS
DNA changes c.490G>A
cDNA.687G>A
g.30252G>A
AA changes G164S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 164
frameshift no
known variant Reference ID: rs121918188
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs868 (pathogenic for Fructose-biphosphatase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5271
6.1681
(flanking)-4.2150
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased30252wt: 0.9960 / mu: 0.9983 (marginal change - not scored)wt: CAGCCGGCTACGCAC
mu: CAGCCAGCTACGCAC		 GCCG|gcta
Donor gained302480.86mu: GTGGCAGCCAGCTAC GGCA|gcca
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      164ALQPGRNLVAAGYALYGSATMLVL
mutated  not conserved    164ALQPGRNLVAASYALYGSATMLV
Ptroglodytes  all identical  ENSPTRG00000021138  164ALQPGRNLVAAGYALYGSATMLV
Mmulatta  all identical  ENSMMUG00000022536  164ALQPGRNLVAAGYALYGSATMLV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000069805  164ALQPGRDLVAAGYALYGSATMLV
Ggallus  all identical  ENSGALG00000012613  174ALQPGRNLVAAGYALYGSATMLV
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0032820  175ALQPGNQLVAAGYALYGSATAIV
Celegans  all identical  K07A3.1  168VLKPGKEMVAAGYALYGSATMVV
Xtropicalis  all identical  ENSXETG00000033240  106ALQPGRNIVAAGYALYGSATMMV
protein features
start (aa)end (aa)featuredetails 
161178STRANDlost
181188STRANDmight get lost (downstream of altered splice site)
189192TURNmight get lost (downstream of altered splice site)
193198STRANDmight get lost (downstream of altered splice site)
208212STRANDmight get lost (downstream of altered splice site)
213216REGIONSubstrate binding.might get lost (downstream of altered splice site)
214219HELIXmight get lost (downstream of altered splice site)
215215CONFLICTG -> A (in Ref. 2; AAA35817 and 5; AAC25774).might get lost (downstream of altered splice site)
222232HELIXmight get lost (downstream of altered splice site)
235237STRANDmight get lost (downstream of altered splice site)
244249REGIONSubstrate binding.might get lost (downstream of altered splice site)
249259HELIXmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
265265BINDINGSubstrate.might get lost (downstream of altered splice site)
269271STRANDmight get lost (downstream of altered splice site)
275277REGIONSubstrate binding.might get lost (downstream of altered splice site)
275277STRANDmight get lost (downstream of altered splice site)
278281TURNmight get lost (downstream of altered splice site)
281281METALMagnesium 3.might get lost (downstream of altered splice site)
282291HELIXmight get lost (downstream of altered splice site)
295297STRANDmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
303305HELIXmight get lost (downstream of altered splice site)
317321STRANDmight get lost (downstream of altered splice site)
322334HELIXmight get lost (downstream of altered splice site)
337337CONFLICTA -> G (in Ref. 5; AAC25774).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1017 / 1017
position (AA) of stopcodon in wt / mu AA sequence 339 / 339
position of stopcodon in wt / mu cDNA 1214 / 1214
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 198 / 198
chromosome 9
strand -1
last intron/exon boundary 1023
theoretical NMD boundary in CDS 775
length of CDS 1017
coding sequence (CDS) position 490
cDNA position
(for ins/del: last normal base / first normal base)		 687
gDNA position
(for ins/del: last normal base / first normal base)		 30252
chromosomal position
(for ins/del: last normal base / first normal base)		 97372280
original gDNA sequence snippet GCCGGAACCTGGTGGCAGCCGGCTACGCACTGTATGGCAGT
altered gDNA sequence snippet GCCGGAACCTGGTGGCAGCCAGCTACGCACTGTATGGCAGT
original cDNA sequence snippet GCCGGAACCTGGTGGCAGCCGGCTACGCACTGTATGGCAGT
altered cDNA sequence snippet GCCGGAACCTGGTGGCAGCCAGCTACGCACTGTATGGCAGT
wildtype AA sequence MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAAGYALYGS ATMLVLAMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*
mutated AA sequence MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAASYALYGS ATMLVLAMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*
speed 0.90 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: 0.999999999735923 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970524)
  • known disease mutation: rs868 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:97372280C>TN/A show variant in all transcripts   IGV
HGNC symbol FBP1
Ensembl transcript ID ENST00000415431
Genbank transcript ID NM_001127628
UniProt peptide P09467
alteration type single base exchange
alteration region CDS
DNA changes c.490G>A
cDNA.720G>A
g.30252G>A
AA changes G164S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 164
frameshift no
known variant Reference ID: rs121918188
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs868 (pathogenic for Fructose-biphosphatase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970524)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5271
6.1681
(flanking)-4.2150
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased30252wt: 0.9960 / mu: 0.9983 (marginal change - not scored)wt: CAGCCGGCTACGCAC
mu: CAGCCAGCTACGCAC		 GCCG|gcta
Donor gained302480.86mu: GTGGCAGCCAGCTAC GGCA|gcca
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      164ALQPGRNLVAAGYALYGSATMLVL
mutated  not conserved    164ALQPGRNLVAASYALYGSATMLV
Ptroglodytes  all identical  ENSPTRG00000021138  164ALQPGRNLVAAGYALYGSATMLV
Mmulatta  all identical  ENSMMUG00000022536  164ALQPGRNLVAAGYALYGSATMLV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000069805  164ALQPGRDLVAAGYALYGSATMLV
Ggallus  all identical  ENSGALG00000012613  174ALQPGRNLVAAGYALYGSATMLV
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0032820  175ALQPGNQLVAAGYALYGSATAIV
Celegans  all identical  K07A3.1  168VLKPGKEMVAAGYALYGSATMVV
Xtropicalis  all identical  ENSXETG00000033240  106ALQPGRNIVAAGYALYGSATMMV
protein features
start (aa)end (aa)featuredetails 
161178STRANDlost
181188STRANDmight get lost (downstream of altered splice site)
189192TURNmight get lost (downstream of altered splice site)
193198STRANDmight get lost (downstream of altered splice site)
208212STRANDmight get lost (downstream of altered splice site)
213216REGIONSubstrate binding.might get lost (downstream of altered splice site)
214219HELIXmight get lost (downstream of altered splice site)
215215CONFLICTG -> A (in Ref. 2; AAA35817 and 5; AAC25774).might get lost (downstream of altered splice site)
222232HELIXmight get lost (downstream of altered splice site)
235237STRANDmight get lost (downstream of altered splice site)
244249REGIONSubstrate binding.might get lost (downstream of altered splice site)
249259HELIXmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
265265BINDINGSubstrate.might get lost (downstream of altered splice site)
269271STRANDmight get lost (downstream of altered splice site)
275277REGIONSubstrate binding.might get lost (downstream of altered splice site)
275277STRANDmight get lost (downstream of altered splice site)
278281TURNmight get lost (downstream of altered splice site)
281281METALMagnesium 3.might get lost (downstream of altered splice site)
282291HELIXmight get lost (downstream of altered splice site)
295297STRANDmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
303305HELIXmight get lost (downstream of altered splice site)
317321STRANDmight get lost (downstream of altered splice site)
322334HELIXmight get lost (downstream of altered splice site)
337337CONFLICTA -> G (in Ref. 5; AAC25774).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1017 / 1017
position (AA) of stopcodon in wt / mu AA sequence 339 / 339
position of stopcodon in wt / mu cDNA 1247 / 1247
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 231 / 231
chromosome 9
strand -1
last intron/exon boundary 1056
theoretical NMD boundary in CDS 775
length of CDS 1017
coding sequence (CDS) position 490
cDNA position
(for ins/del: last normal base / first normal base)		 720
gDNA position
(for ins/del: last normal base / first normal base)		 30252
chromosomal position
(for ins/del: last normal base / first normal base)		 97372280
original gDNA sequence snippet GCCGGAACCTGGTGGCAGCCGGCTACGCACTGTATGGCAGT
altered gDNA sequence snippet GCCGGAACCTGGTGGCAGCCAGCTACGCACTGTATGGCAGT
original cDNA sequence snippet GCCGGAACCTGGTGGCAGCCGGCTACGCACTGTATGGCAGT
altered cDNA sequence snippet GCCGGAACCTGGTGGCAGCCAGCTACGCACTGTATGGCAGT
wildtype AA sequence MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAAGYALYGS ATMLVLAMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*
mutated AA sequence MADQAPFDTD VNTLTRFVME EGRKARGTGE LTQLLNSLCT AVKAISSAVR KAGIAHLYGI
AGSTNVTGDQ VKKLDVLSND LVMNMLKSSF ATCVLVSEED KHAIIVEPEK RGKYVVCFDP
LDGSSNIDCL VSVGTIFGIY RKKSTDEPSE KDALQPGRNL VAASYALYGS ATMLVLAMDC
GVNCFMLDPA IGEFILVDKD VKIKKKGKIY SLNEGYARDF DPAVTEYIQR KKFPPDNSAP
YGARYVGSMV ADVHRTLVYG GIFLYPANKK SPNGKLRLLY ECNPMAYVME KAGGMATTGK
EAVLDVIPTD IHQRAPVILG SPDDVLEFLK VYEKHSAQ*
speed 0.86 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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