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: ENST00000374855
Querying Taster for transcript #2: ENST00000374853
MT speed 0 s - this script 3.455935 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ALDOBdisease_causing_automatic0.999999933847234simple_aaeaffected0N335Ksingle base exchangers78340951show file
ALDOBdisease_causing_automatic0.999999999999739without_aaeaffected0single base exchangers78340951show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999933847234 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900014)
  • known disease mutation: rs469 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:104184181G>CN/A show variant in all transcripts   IGV
HGNC symbol ALDOB
Ensembl transcript ID ENST00000374855
Genbank transcript ID NM_000035
UniProt peptide P05062
alteration type single base exchange
alteration region CDS
DNA changes c.1005C>G
cDNA.1130C>G
g.13925C>G
AA changes N335K Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 335
frameshift no
known variant Reference ID: rs78340951
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC01414

known disease mutation: rs469 (pathogenic for Hereditary fructosuria|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOXA1, Transcription Factor, FOXA1 Transcription Factor Binding
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
RXRA, Transcription Factor, RXRA Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9840.183
0.620.485
(flanking)4.9241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased13915wt: 0.73 / mu: 0.81wt: CTCCTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGG
mu: CTCCTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGG		 tctt|CTAG
Acc marginally increased13918wt: 0.9803 / mu: 0.9828 (marginal change - not scored)wt: CTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCA
mu: CTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCA		 tcta|GGCT
Acc marginally increased13917wt: 0.9767 / mu: 0.9821 (marginal change - not scored)wt: CCTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGGCC
mu: CCTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCC		 ttct|AGGC
Acc increased13924wt: 0.83 / mu: 0.96wt: CATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCAAAGGAC
mu: CATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCAAAGGAC		 ctaa|CTGC
Donor marginally increased13926wt: 0.8915 / mu: 0.9018 (marginal change - not scored)wt: CTAACTGCCAGGCGG
mu: CTAAGTGCCAGGCGG		 AACT|gcca
Donor marginally increased13919wt: 0.9613 / mu: 0.9973 (marginal change - not scored)wt: TTCTAGGCTAACTGC
mu: TTCTAGGCTAAGTGC		 CTAG|gcta
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      335TQEAFMKRAMANCQAAKGQYVHTG
mutated  not conserved    335TQEAFMKRAMAKCQAAKGQYVHT
Ptroglodytes  all identical  ENSPTRG00000021201  335TQEAFMKRAVANCQAAKGQYVHT
Mmulatta  all identical  ENSMMUG00000023796  335TQEAFMKRAVANCQAAKGQYIHT
Fcatus  all identical  ENSFCAG00000001417  335ANCQAAKGQYVHS
Mmusculus  all identical  ENSMUSG00000028307  335TQEAFMKRAMANCQAAQGQYVHT
Ggallus  all identical  ENSGALG00000015544  335AQEAFCKRAQINSLACRGQYVTS
Trubripes  all identical  ENSTRUG00000008103  352AQEAFCKRAKINGLASKGEYNPS
Drerio  all identical  ENSDARG00000053684  335SQDAFVTRAKINSLASKGEYKPS
Dmelanogaster  all identical  FBgn0000064  334GQNELLKRAKANGEAACGNYTAG
Celegans  all identical  T05D4.1  336AQEVLLHRAQVNSLASVGKYTGD
Xtropicalis  all identical  ENSXETG00000024058  353AQEAFVKRAKINGLATLGKYVPS
protein features
start (aa)end (aa)featuredetails 
321338HELIXlost
339341TURNmight get lost (downstream of altered splice site)
348348CONFLICTS -> C (in Ref. 4; BAA00125).might get lost (downstream of altered splice site)
351354HELIXmight get lost (downstream of altered splice site)
364364SITENecessary for preference for fructose 1,6-bisphosphate over fructose 1- phosphate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1095 / 1095
position (AA) of stopcodon in wt / mu AA sequence 365 / 365
position of stopcodon in wt / mu cDNA 1220 / 1220
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 126 / 126
chromosome 9
strand -1
last intron/exon boundary 1125
theoretical NMD boundary in CDS 949
length of CDS 1095
coding sequence (CDS) position 1005
cDNA position
(for ins/del: last normal base / first normal base)		 1130
gDNA position
(for ins/del: last normal base / first normal base)		 13925
chromosomal position
(for ins/del: last normal base / first normal base)		 104184181
original gDNA sequence snippet ATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCAAAGGACA
altered gDNA sequence snippet ATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCAAAGGACA
original cDNA sequence snippet ATGAAGCGGGCCATGGCTAACTGCCAGGCGGCCAAAGGACA
altered cDNA sequence snippet ATGAAGCGGGCCATGGCTAAGTGCCAGGCGGCCAAAGGACA
wildtype AA sequence MAHRFPALTQ EQKKELSEIA QSIVANGKGI LAADESVGTM GNRLQRIKVE NTEENRRQFR
EILFSVDSSI NQSIGGVILF HETLYQKDSQ GKLFRNILKE KGIVVGIKLD QGGAPLAGTN
KETTIQGLDG LSERCAQYKK DGVDFGKWRA VLRIADQCPS SLAIQENANA LARYASICQQ
NGLVPIVEPE VIPDGDHDLE HCQYVTEKVL AAVYKALNDH HVYLEGTLLK PNMVTAGHAC
TKKYTPEQVA MATVTALHRT VPAAVPGICF LSGGMSEEDA TLNLNAINLC PLPKPWKLSF
SYGRALQASA LAAWGGKAAN KEATQEAFMK RAMANCQAAK GQYVHTGSSG AASTQSLFTA
CYTY*
mutated AA sequence MAHRFPALTQ EQKKELSEIA QSIVANGKGI LAADESVGTM GNRLQRIKVE NTEENRRQFR
EILFSVDSSI NQSIGGVILF HETLYQKDSQ GKLFRNILKE KGIVVGIKLD QGGAPLAGTN
KETTIQGLDG LSERCAQYKK DGVDFGKWRA VLRIADQCPS SLAIQENANA LARYASICQQ
NGLVPIVEPE VIPDGDHDLE HCQYVTEKVL AAVYKALNDH HVYLEGTLLK PNMVTAGHAC
TKKYTPEQVA MATVTALHRT VPAAVPGICF LSGGMSEEDA TLNLNAINLC PLPKPWKLSF
SYGRALQASA LAAWGGKAAN KEATQEAFMK RAMAKCQAAK GQYVHTGSSG AASTQSLFTA
CYTY*
speed 0.81 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: without_aae, prob: 0.999999999999739 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM900014)
  • known disease mutation: rs469 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:104184181G>CN/A show variant in all transcripts   IGV
HGNC symbol ALDOB
Ensembl transcript ID ENST00000374853
Genbank transcript ID N/A
UniProt peptide P05062
alteration type single base exchange
alteration region intron
DNA changes g.13925C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs78340951
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC01414

known disease mutation: rs469 (pathogenic for Hereditary fructosuria|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900014)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOXA1, Transcription Factor, FOXA1 Transcription Factor Binding
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
RXRA, Transcription Factor, RXRA Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9840.183
0.620.485
(flanking)4.9241
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased13915wt: 0.73 / mu: 0.81wt: CTCCTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGG
mu: CTCCTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGG		 tctt|CTAG
Acc marginally increased13918wt: 0.9803 / mu: 0.9828 (marginal change - not scored)wt: CTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCA
mu: CTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCA		 tcta|GGCT
Acc marginally increased13917wt: 0.9767 / mu: 0.9821 (marginal change - not scored)wt: CCTCTCTCATATTTGTCTTCTAGGCTAACTGCCAGGCGGCC
mu: CCTCTCTCATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCC		 ttct|AGGC
Acc increased13924wt: 0.83 / mu: 0.96wt: CATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCAAAGGAC
mu: CATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCAAAGGAC		 ctaa|CTGC
Donor marginally increased13926wt: 0.8915 / mu: 0.9018 (marginal change - not scored)wt: CTAACTGCCAGGCGG
mu: CTAAGTGCCAGGCGG		 AACT|gcca
Donor marginally increased13919wt: 0.9613 / mu: 0.9973 (marginal change - not scored)wt: TTCTAGGCTAACTGC
mu: TTCTAGGCTAAGTGC		 CTAG|gcta
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
199219HELIXmight get lost (downstream of altered splice site)
224226HELIXmight get lost (downstream of altered splice site)
230230ACT_SITESchiff-base intermediate with dihydroxyacetone-P.might get lost (downstream of altered splice site)
246260HELIXmight get lost (downstream of altered splice site)
250250CONFLICTA -> D (in Ref. 9; CAA25072).might get lost (downstream of altered splice site)
267271STRANDmight get lost (downstream of altered splice site)
277289HELIXmight get lost (downstream of altered splice site)
278278CONFLICTE -> D (in Ref. 4; BAA00125).might get lost (downstream of altered splice site)
290292STRANDmight get lost (downstream of altered splice site)
296303STRANDmight get lost (downstream of altered splice site)
304306HELIXmight get lost (downstream of altered splice site)
308314HELIXmight get lost (downstream of altered splice site)
309309CONFLICTS -> V (in Ref. 3; no nucleotide entry).might get lost (downstream of altered splice site)
318320HELIXmight get lost (downstream of altered splice site)
321338HELIXmight get lost (downstream of altered splice site)
339341TURNmight get lost (downstream of altered splice site)
348348CONFLICTS -> C (in Ref. 4; BAA00125).might get lost (downstream of altered splice site)
351354HELIXmight get lost (downstream of altered splice site)
364364SITENecessary for preference for fructose 1,6-bisphosphate over fructose 1- phosphate.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 77 / 77
chromosome 9
strand -1
last intron/exon boundary 718
theoretical NMD boundary in CDS 591
length of CDS 672
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 13925
chromosomal position
(for ins/del: last normal base / first normal base)		 104184181
original gDNA sequence snippet ATATTTGTCTTCTAGGCTAACTGCCAGGCGGCCAAAGGACA
altered gDNA sequence snippet ATATTTGTCTTCTAGGCTAAGTGCCAGGCGGCCAAAGGACA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAHRFPALTQ EQKKDSQGKL FRNILKEKGI VVGIKLDQGG APLAGTNKET TIQGLDGLSE
RCAQYKKDGV DFGKWRAVLR IADQCPSSLA IQENANALAR YASICQQNGL VPIVEPEVIP
DGDHDLEHCQ YVTEKVLAAV YKALNDHHVY LEGTLLKPNM VTAGHACTKK YTPEQVAMAT
VTALHRTVPA AVPGICFLSG GMSEEDATLN LNAIPTRVQC PPA*
mutated AA sequence N/A
speed 0.65 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