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 4.077332 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHST6disease_causing_automatic0.999999981899508simple_aaeaffected0C102Gsingle base exchangers121917822show file
CHST6disease_causing_automatic0.999999981899508simple_aaeaffected0C102Gsingle base exchangers121917822show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999981899508 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040401)
  • known disease mutation: rs5076 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:75513423A>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.304T>G
cDNA.484T>G
g.15860T>G
AA changes C102G Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 102
frameshift no
known variant Reference ID: rs121917822
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5076 (pathogenic for Macular corneal dystrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0781
4.1961
(flanking)0.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased15859wt: 0.77 / mu: 0.95wt: CTGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGA
mu: CTGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGA		 cctg|TGCG
Donor increased15860wt: 0.43 / mu: 0.52wt: TCCTGTGCGACATGG
mu: TCCTGGGCGACATGG		 CTGT|gcga
distance from splice site 320
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      102AVRDLVRSVFLCDMDVFDAYLPWR
mutated  not conserved    102AVRDLVRSVFLGDMDVFDAYLPW
Ptroglodytes  all identical  ENSPTRG00000042548  102AVRDLVRSVFLCDMDVFDAYLPW
Mmulatta  all identical  ENSMMUG00000001563  102AVRDLVRSVFLCDMDVFDAYLPW
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031952  102AVRDLIRSVFLCDMDVFDAYLPW
Ggallus  all identical  ENSGALG00000000913  104AVRDLVRSVFLCDMSVFDAYMPW
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000061357  142AVRDTIRSIFQCDMSVMDSYIRQ
Dmelanogaster  all identical  FBgn0051637  244QNL-KNLLNCDYADMIDYLNF
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003576  103AVRDLIRSVFLCDMSVFDAYIPK
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 304
cDNA position
(for ins/del: last normal base / first normal base)		 484
gDNA position
(for ins/del: last normal base / first normal base)		 15860
chromosomal position
(for ins/del: last normal base / first normal base)		 75513423
original gDNA sequence snippet TGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGAT
altered gDNA sequence snippet TGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGAT
original cDNA sequence snippet TGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGAT
altered cDNA sequence snippet TGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGAT
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 LGDMDVFDAY 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 1.09 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: 0.999999981899508 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040401)
  • known disease mutation: rs5076 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:75513423A>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.304T>G
cDNA.996T>G
g.15860T>G
AA changes C102G Score: 159 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 102
frameshift no
known variant Reference ID: rs121917822
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5076 (pathogenic for Macular corneal dystrophy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040401)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.0781
4.1961
(flanking)0.5261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased15859wt: 0.77 / mu: 0.95wt: CTGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGA
mu: CTGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGA		 cctg|TGCG
Donor increased15860wt: 0.43 / mu: 0.52wt: TCCTGTGCGACATGG
mu: TCCTGGGCGACATGG		 CTGT|gcga
distance from splice site 320
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      102AVRDLVRSVFLCDMDVFDAYLPWR
mutated  not conserved    102AVRDLVRSVFLGDMDVFDAYLPW
Ptroglodytes  all identical  ENSPTRG00000042548  102AVRDLVRSVFLCDMDVFDAYLPW
Mmulatta  all identical  ENSMMUG00000001563  102AVRDLVRSVFLCDMDVFDAYLPW
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031952  102AVRDLIRSVFLCDMDVFDAYLPW
Ggallus  all identical  ENSGALG00000000913  104AVRDLVRSVFLCDMSVFDAYMPW
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000061357  142AVRDTIRSIFQCDMSVMDSYIRQ
Dmelanogaster  all identical  FBgn0051637  244QNL-KNLLNCDYADMIDYLNF
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003576  103AVRDLIRSVFLCDMSVFDAYIPK
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 304
cDNA position
(for ins/del: last normal base / first normal base)		 996
gDNA position
(for ins/del: last normal base / first normal base)		 15860
chromosomal position
(for ins/del: last normal base / first normal base)		 75513423
original gDNA sequence snippet TGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGAT
altered gDNA sequence snippet TGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGAT
original cDNA sequence snippet TGGTGCGCTCCGTCTTCCTGTGCGACATGGACGTGTTTGAT
altered cDNA sequence snippet TGGTGCGCTCCGTCTTCCTGGGCGACATGGACGTGTTTGAT
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 LGDMDVFDAY 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 1.05 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