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: ENST00000268695
Querying Taster for transcript #2: ENST00000542788
MT speed 1.47 s - this script 3.471082 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GALNSdisease_causing_automatic0.999887996865815simple_aae0F69Vsingle base exchangers118204445show file
GALNSdisease_causing_automatic1without_aae0single base exchangers118204445show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999887996865815 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970576)
  • known disease mutation: rs710 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88909153A>CN/A show variant in all transcripts   IGV
HGNC symbol GALNS
Ensembl transcript ID ENST00000268695
Genbank transcript ID NM_000512
UniProt peptide P34059
alteration type single base exchange
alteration region CDS
DNA changes c.205T>G
cDNA.294T>G
g.14226T>G
AA changes F69V Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 69
frameshift no
known variant Reference ID: rs118204445
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs710 (pathogenic for Mucopolysaccharidosis, MPS-IV-A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8061
1.2040.85
(flanking)-1.9240.153
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 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      69NLDRMAAEGLLFPNFYSANPLCSP
mutated  not conserved    69RMAAEGLLVPNFYSANPLCS
Ptroglodytes  all identical  ENSPTRG00000008467  69RMAAEGMLFPNFYSANPLCS
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000013017  29NLDRMAAEGTLFPNFYSANPLCS
Mmusculus  all identical  ENSMUSG00000015027  66RMAAEGMLFPSFYSANPLCS
Ggallus  all identical  ENSGALG00000006282  67NLDQMASEGMLFLDFYAANPLCS
Trubripes  not conserved  ENSTRUG00000017249  73NLDAMAAQGMLLLNFYTANPLCS
Drerio  all identical  ENSDARG00000051853  60YLDLMAAQGMLFPNFYTANPLCS
Dmelanogaster  not conserved  FBgn0033763  66NIDALAYSGIILNRY
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011256  66NLDKMASEGMLFPNFYTANPLCS
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1569 / 1569
position (AA) of stopcodon in wt / mu AA sequence 523 / 523
position of stopcodon in wt / mu cDNA 1658 / 1658
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 90 / 90
chromosome 16
strand -1
last intron/exon boundary 1572
theoretical NMD boundary in CDS 1432
length of CDS 1569
coding sequence (CDS) position 205
cDNA position
(for ins/del: last normal base / first normal base)		 294
gDNA position
(for ins/del: last normal base / first normal base)		 14226
chromosomal position
(for ins/del: last normal base / first normal base)		 88909153
original gDNA sequence snippet TGGCTGCAGAAGGGCTGCTTTTCCCAAACTTCTATTCTGCC
altered gDNA sequence snippet TGGCTGCAGAAGGGCTGCTTGTCCCAAACTTCTATTCTGCC
original cDNA sequence snippet TGGCTGCAGAAGGGCTGCTTTTCCCAAACTTCTATTCTGCC
altered cDNA sequence snippet TGGCTGCAGAAGGGCTGCTTGTCCCAAACTTCTATTCTGCC
wildtype AA sequence MAAVVAATRW WQLLLVLSAA GMGASGAPQP PNILLLLMDD MGWGDLGVYG EPSRETPNLD
RMAAEGLLFP NFYSANPLCS PSRAALLTGR LPIRNGFYTT NAHARNAYTP QEIVGGIPDS
EQLLPELLKK AGYVSKIVGK WHLGHRPQFH PLKHGFDEWF GSPNCHFGPY DNKARPNIPV
YRDWEMVGRY YEEFPINLKT GEANLTQIYL QEALDFIKRQ ARHHPFFLYW AVDATHAPVY
ASKPFLGTSQ RGRYGDAVRE IDDSIGKILE LLQDLHVADN TFVFFTSDNG AALISAPEQG
GSNGPFLCGK QTTFEGGMRE PALAWWPGHV TAGQVSHQLG SIMDLFTTSL ALAGLTPPSD
RAIDGLNLLP TLLQGRLMDR PIFYYRGDTL MAATLGQHKA HFWTWTNSWE NFRQGIDFCP
GQNVSGVTTH NLEDHTKLPL IFHLGRDPGE RFPLSFASAE YQEALSRITS VVQQHQEALV
PAQPQLNVCN WAVMNWAPPG CEKLGKCLTP PESIPKKCLW SH*
mutated AA sequence MAAVVAATRW WQLLLVLSAA GMGASGAPQP PNILLLLMDD MGWGDLGVYG EPSRETPNLD
RMAAEGLLVP NFYSANPLCS PSRAALLTGR LPIRNGFYTT NAHARNAYTP QEIVGGIPDS
EQLLPELLKK AGYVSKIVGK WHLGHRPQFH PLKHGFDEWF GSPNCHFGPY DNKARPNIPV
YRDWEMVGRY YEEFPINLKT GEANLTQIYL QEALDFIKRQ ARHHPFFLYW AVDATHAPVY
ASKPFLGTSQ RGRYGDAVRE IDDSIGKILE LLQDLHVADN TFVFFTSDNG AALISAPEQG
GSNGPFLCGK QTTFEGGMRE PALAWWPGHV TAGQVSHQLG SIMDLFTTSL ALAGLTPPSD
RAIDGLNLLP TLLQGRLMDR PIFYYRGDTL MAATLGQHKA HFWTWTNSWE NFRQGIDFCP
GQNVSGVTTH NLEDHTKLPL IFHLGRDPGE RFPLSFASAE YQEALSRITS VVQQHQEALV
PAQPQLNVCN WAVMNWAPPG CEKLGKCLTP PESIPKKCLW SH*
speed 0.83 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: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM970576)
  • known disease mutation: rs710 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88909153A>CN/A show variant in all transcripts   IGV
HGNC symbol GALNS
Ensembl transcript ID ENST00000542788
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.14226T>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs118204445
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs710 (pathogenic for Mucopolysaccharidosis, MPS-IV-A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970576)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8061
1.2040.85
(flanking)-1.9240.153
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 1651
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
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 1 / 1
chromosome 16
strand -1
last intron/exon boundary 1258
theoretical NMD boundary in CDS 1207
length of CDS 1344
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)		 14226
chromosomal position
(for ins/del: last normal base / first normal base)		 88909153
original gDNA sequence snippet TGGCTGCAGAAGGGCTGCTTTTCCCAAACTTCTATTCTGCC
altered gDNA sequence snippet TGGCTGCAGAAGGGCTGCTTGTCCCAAACTTCTATTCTGCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAAVVAATRW WQLLLVLSAA GMGASGAPGQ RAYTPQEIVG GIPDSEQLLP ELLKKAGYVS
KIVGKWHLGH RPQFHPLKHG FDEWFGSPNC HFGPYDNKAR PNIPVYRDWE MVGRYYEEFP
INLKTGEANL TQIYLQEALD FIKRQARHHP FFLYWAVDAT HAPVYASKPF LGTSQRGRYG
DAVREIDDSI GKILELLQDL HVADNTFVFF TSDNGAALIS APEQGGSNGP FLCGKQTTFE
GGMREPALAW WPGHVTAGQV SHQLGSIMDL FTTSLALAGL TPPSDRAIDG LNLLPTLLQG
RLMDRPIFYY RGDTLMAATL GQHKAHFWTW TNSWENFRQG IDFCPGQNVS GVTTHNLEDH
TKLPLIFHLG RDPGERFPLS FASAEYQEAL SRITSVVQQH QEALVPAQPQ LNVCNWAVMN
WAPPGCEKLG KCLTPPESIP KKCLWSH*
mutated AA sequence N/A
speed 0.64 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