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: ENST00000332272
Querying Taster for transcript #2: ENST00000390664
MT speed 0 s - this script 4.013544 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHST6disease_causing_automatic0.999995939273558simple_aaeaffected0Y110Csingle base exchangers72547544show file
CHST6disease_causing_automatic0.999995939273558simple_aaeaffected0Y110Csingle base exchangers72547544show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999995939273558 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040697)
  • known disease mutation: rs5077 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:75513398T>CN/A show variant in all transcripts   IGV
HGNC symbol CHST6
Ensembl transcript ID ENST00000332272
Genbank transcript ID NM_021615
UniProt peptide Q9GZX3
alteration type single base exchange
alteration region CDS
DNA changes c.329A>G
cDNA.509A>G
g.15885A>G
AA changes Y110C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 110
frameshift no
known variant Reference ID: rs72547544
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5077 (pathogenic for Macular corneal dystrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5561
2.6031
(flanking)2.5761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased15893wt: 0.9102 / mu: 0.9190 (marginal change - not scored)wt: TGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGAC
mu: TGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGAC		 cctt|GGCG
Acc marginally increased15890wt: 0.2970 / mu: 0.3297 (marginal change - not scored)wt: ACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCC
mu: ACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCC		 ctgc|CTTG
Acc increased15892wt: 0.27 / mu: 0.42wt: GTGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGA
mu: GTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGA		 gcct|TGGC
Acc increased15894wt: 0.37 / mu: 0.46wt: GTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGACC
mu: GTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGACC		 cttg|GCGC
distance from splice site 345
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      110VFLCDMDVFDAYLPWRRNLSDLFQ
mutated  not conserved    110VFLCDMDVFDACLPWRRNLSDL
Ptroglodytes  all identical  ENSPTRG00000042548  110VFLCDMDVFDAYLPWRRNLSDL
Mmulatta  all identical  ENSMMUG00000001563  110VFLCDMDVFDAYLPWRRNLSDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031952  110VFLCDMDVFDAYLPWRRNISDL
Ggallus  all identical  ENSGALG00000000913  112VFLCDMSVFDAYMPWKRNLSDLF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000061357  150IFQCDMSVMDSYIRQPQNISNLF
Dmelanogaster  all identical  FBgn0051637  252LLNCDYADMIDYLNFGKTHTYLF
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003576  111VFLCDMSVFDAYIPKRMNVSELF
protein features
start (aa)end (aa)featuredetails 
27395TOPO_DOMLumenal (Potential).lost
116116CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
202210NP_BINDPAPS (By similarity).might get lost (downstream of altered splice site)
229229CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
305305CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
328328CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1188 / 1188
position (AA) of stopcodon in wt / mu AA sequence 396 / 396
position of stopcodon in wt / mu cDNA 1368 / 1368
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 181 / 181
chromosome 16
strand -1
last intron/exon boundary 165
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1188
coding sequence (CDS) position 329
cDNA position
(for ins/del: last normal base / first normal base)		 509
gDNA position
(for ins/del: last normal base / first normal base)		 15885
chromosomal position
(for ins/del: last normal base / first normal base)		 75513398
original gDNA sequence snippet CATGGACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACC
altered gDNA sequence snippet CATGGACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACC
original cDNA sequence snippet CATGGACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACC
altered cDNA sequence snippet CATGGACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACC
wildtype AA sequence MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVRDLVRSVF LCDMDVFDAY LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*
mutated AA sequence MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVRDLVRSVF LCDMDVFDAC LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*
speed 1.24 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: 0.999995939273558 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040697)
  • known disease mutation: rs5077 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:75513398T>CN/A show variant in all transcripts   IGV
HGNC symbol CHST6
Ensembl transcript ID ENST00000390664
Genbank transcript ID N/A
UniProt peptide Q9GZX3
alteration type single base exchange
alteration region CDS
DNA changes c.329A>G
cDNA.1021A>G
g.15885A>G
AA changes Y110C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 110
frameshift no
known variant Reference ID: rs72547544
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5077 (pathogenic for Macular corneal dystrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040697)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.5561
2.6031
(flanking)2.5761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased15893wt: 0.9102 / mu: 0.9190 (marginal change - not scored)wt: TGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGAC
mu: TGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGAC		 cctt|GGCG
Acc marginally increased15890wt: 0.2970 / mu: 0.3297 (marginal change - not scored)wt: ACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCC
mu: ACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCC		 ctgc|CTTG
Acc increased15892wt: 0.27 / mu: 0.42wt: GTGTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGA
mu: GTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGA		 gcct|TGGC
Acc increased15894wt: 0.37 / mu: 0.46wt: GTTTGATGCCTATCTGCCTTGGCGCCGCAACCTGTCCGACC
mu: GTTTGATGCCTGTCTGCCTTGGCGCCGCAACCTGTCCGACC		 cttg|GCGC
distance from splice site 345
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      110VFLCDMDVFDAYLPWRRNLSDLFQ
mutated  not conserved    110VFLCDMDVFDACLPWRRNLSDL
Ptroglodytes  all identical  ENSPTRG00000042548  110VFLCDMDVFDAYLPWRRNLSDL
Mmulatta  all identical  ENSMMUG00000001563  110VFLCDMDVFDAYLPWRRNLSDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031952  110VFLCDMDVFDAYLPWRRNISDL
Ggallus  all identical  ENSGALG00000000913  112VFLCDMSVFDAYMPWKRNLSDLF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000061357  150IFQCDMSVMDSYIRQPQNISNLF
Dmelanogaster  all identical  FBgn0051637  252LLNCDYADMIDYLNFGKTHTYLF
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003576  111VFLCDMSVFDAYIPKRMNVSELF
protein features
start (aa)end (aa)featuredetails 
27395TOPO_DOMLumenal (Potential).lost
116116CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
202210NP_BINDPAPS (By similarity).might get lost (downstream of altered splice site)
229229CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
305305CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
328328CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1188 / 1188
position (AA) of stopcodon in wt / mu AA sequence 396 / 396
position of stopcodon in wt / mu cDNA 1880 / 1880
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 693 / 693
chromosome 16
strand -1
last intron/exon boundary 677
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1188
coding sequence (CDS) position 329
cDNA position
(for ins/del: last normal base / first normal base)		 1021
gDNA position
(for ins/del: last normal base / first normal base)		 15885
chromosomal position
(for ins/del: last normal base / first normal base)		 75513398
original gDNA sequence snippet CATGGACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACC
altered gDNA sequence snippet CATGGACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACC
original cDNA sequence snippet CATGGACGTGTTTGATGCCTATCTGCCTTGGCGCCGCAACC
altered cDNA sequence snippet CATGGACGTGTTTGATGCCTGTCTGCCTTGGCGCCGCAACC
wildtype AA sequence MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVRDLVRSVF LCDMDVFDAY LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*
mutated AA sequence MWLPRVSSTA VTALLLAQTF LLLFLVSRPG PSSPAGGEAR VHVLVLSSWR SGSSFVGQLF
NQHPDVFYLM EPAWHVWTTL SQGSAATLHM AVRDLVRSVF LCDMDVFDAC LPWRRNLSDL
FQWAVSRALC SPPACSAFPR GAISSEAVCK PLCARQSFTL AREACRSYSH VVLKEVRFFN
LQVLYPLLSD PALNLRIVHL VRDPRAVLRS REQTAKALAR DNGIVLGTNG TWVEADPGLR
VVREVCRSHV RIAEAATLKP PPFLRGRYRL VRFEDLAREP LAEIRALYAF TGLSLTPQLE
AWIHNITHGS GPGARREAFK TSSRNALNVS QAWRHALPFA KIRRVQELCA GALQLLGYRP
VYSEDEQRNL ALDLVLPRGL NGFTWASSTA SHPRN*
speed 0.77 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

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