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: ENST00000366837
Querying Taster for transcript #2: ENST00000272167
MT speed 0 s - this script 3.517932 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPHX1polymorphism_automatic0.999999030377786simple_aaeaffectedY113Hsingle base exchangers1051740show file
EPHX1polymorphism_automatic0.999999030377786simple_aaeaffectedY113Hsingle base exchangers1051740show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 9.69622214185287e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM940369)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:226019633T>CN/A show variant in all transcripts   IGV
HGNC symbol EPHX1
Ensembl transcript ID ENST00000366837
Genbank transcript ID NM_000120
UniProt peptide P07099
alteration type single base exchange
alteration region CDS
DNA changes c.337T>C
cDNA.533T>C
g.21840T>C
AA changes Y113H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs1051740
databasehomozygous (C/C)heterozygousallele carriers
1000G2929851277
ExAC63572005326410

known disease mutation at this position, please check HGMD for details (HGMD ID CM940369)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6220.051
4.9670.999
(flanking)2.3251
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 increased21837wt: 0.9269 / mu: 0.9320 (marginal change - not scored)wt: TCAACAGATACCCTC
mu: TCAACAGACACCCTC		 AACA|gata
Donor gained218350.57mu: TCTCAACAGACACCC TCAA|caga
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113DWKKQVEILNRYPHFKTKIEGLDI
mutated  all conserved    113DWKKQVEILNRHPHFKTKI
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000005782  113NWKKQVEILNRYPHFKTKI
Fcatus  all identical  ENSFCAG00000006965  111YSHFKTRIEGLD
Mmusculus  all identical  ENSMUSG00000038776  113DWRKQVEILNQYPHFKTKI
Ggallus  all identical  ENSGALG00000009291  121NWKKQVEVLNKYPHFKTK
Trubripes  all identical  ENSTRUG00000006133  115DWKKQVAVLNKYPHYKTKIEGLD
Drerio  all identical  ENSDARG00000042854  113NWGKQLDKLNKYPHFKTKI
Dmelanogaster  not conserved  FBgn0034405  122KWSEREEYLKKLDHYQTEIQGLK
Celegans  all conserved  W01A11.1  114DWRKQEATINQFPQFKTEIEGLQ
Xtropicalis  all conserved  ENSXETG00000022654  113NWRKQLDILNKFPHFKTKI
protein features
start (aa)end (aa)featuredetails 
112112CONFLICTR -> K (in Ref. 10).might get lost (downstream of altered splice site)
148148CONFLICTH -> N (in Ref. 3 and 10).might get lost (downstream of altered splice site)
243243CONFLICTV -> L (in Ref. 10).might get lost (downstream of altered splice site)
295295MOD_RESOmega-N-methylated arginine (By similarity).might get lost (downstream of altered splice site)
348348CONFLICTK -> S (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
406406CONFLICTL -> F (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
420420CONFLICTL -> V (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1368 / 1368
position (AA) of stopcodon in wt / mu AA sequence 456 / 456
position of stopcodon in wt / mu cDNA 1564 / 1564
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 197 / 197
chromosome 1
strand 1
last intron/exon boundary 1363
theoretical NMD boundary in CDS 1116
length of CDS 1368
coding sequence (CDS) position 337
cDNA position
(for ins/del: last normal base / first normal base)		 533
gDNA position
(for ins/del: last normal base / first normal base)		 21840
chromosomal position
(for ins/del: last normal base / first normal base)		 226019633
original gDNA sequence snippet AGGTGGAGATTCTCAACAGATACCCTCACTTCAAGACTAAG
altered gDNA sequence snippet AGGTGGAGATTCTCAACAGACACCCTCACTTCAAGACTAAG
original cDNA sequence snippet AGGTGGAGATTCTCAACAGATACCCTCACTTCAAGACTAAG
altered cDNA sequence snippet AGGTGGAGATTCTCAACAGACACCCTCACTTCAAGACTAAG
wildtype AA sequence MWLEILLTSV LGFAIYWFIS RDKEETLPLE DGWWGPGTRS AAREDDSIRP FKVETSDEEI
HDLHQRIDKF RFTPPLEDSC FHYGFNSNYL KKVISYWRNE FDWKKQVEIL NRYPHFKTKI
EGLDIHFIHV KPPQLPAGHT PKPLLMVHGW PGSFYEFYKI IPLLTDPKNH GLSDEHVFEV
ICPSIPGYGF SEASSKKGFN SVATARIFYK LMLRLGFQEF YIQGGDWGSL ICTNMAQLVP
SHVKGLHLNM ALVLSNFSTL TLLLGQRFGR FLGLTERDVE LLYPVKEKVF YSLMRESGYM
HIQCTKPDTV GSALNDSPVG LAAYILEKFS TWTNTEFRYL EDGGLERKFS LDDLLTNVML
YWTTGTIISS QRFYKENLGQ GWMTQKHERM KVYVPTGFSA FPFELLHTPE KWVRFKYPKL
ISYSYMVRGG HFAAFEEPEL LAQDIRKFLS VLERQ*
mutated AA sequence MWLEILLTSV LGFAIYWFIS RDKEETLPLE DGWWGPGTRS AAREDDSIRP FKVETSDEEI
HDLHQRIDKF RFTPPLEDSC FHYGFNSNYL KKVISYWRNE FDWKKQVEIL NRHPHFKTKI
EGLDIHFIHV KPPQLPAGHT PKPLLMVHGW PGSFYEFYKI IPLLTDPKNH GLSDEHVFEV
ICPSIPGYGF SEASSKKGFN SVATARIFYK LMLRLGFQEF YIQGGDWGSL ICTNMAQLVP
SHVKGLHLNM ALVLSNFSTL TLLLGQRFGR FLGLTERDVE LLYPVKEKVF YSLMRESGYM
HIQCTKPDTV GSALNDSPVG LAAYILEKFS TWTNTEFRYL EDGGLERKFS LDDLLTNVML
YWTTGTIISS QRFYKENLGQ GWMTQKHERM KVYVPTGFSA FPFELLHTPE KWVRFKYPKL
ISYSYMVRGG HFAAFEEPEL LAQDIRKFLS VLERQ*
speed 0.85 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

polymorphism

 Model: simple_aae, prob: 9.69622214185287e-07 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM940369)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:226019633T>CN/A show variant in all transcripts   IGV
HGNC symbol EPHX1
Ensembl transcript ID ENST00000272167
Genbank transcript ID NM_001136018
UniProt peptide P07099
alteration type single base exchange
alteration region CDS
DNA changes c.337T>C
cDNA.417T>C
g.21840T>C
AA changes Y113H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 113
frameshift no
known variant Reference ID: rs1051740
databasehomozygous (C/C)heterozygousallele carriers
1000G2929851277
ExAC63572005326410

known disease mutation at this position, please check HGMD for details (HGMD ID CM940369)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6220.051
4.9670.999
(flanking)2.3251
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 increased21837wt: 0.9269 / mu: 0.9320 (marginal change - not scored)wt: TCAACAGATACCCTC
mu: TCAACAGACACCCTC		 AACA|gata
Donor gained218350.57mu: TCTCAACAGACACCC TCAA|caga
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      113DWKKQVEILNRYPHFKTKIEGLDI
mutated  all conserved    113DWKKQVEILNRHPHFKTKI
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000005782  113NWKKQVEILNRYPHFKTKI
Fcatus  all identical  ENSFCAG00000006965  111YSHFKTRIEGLD
Mmusculus  all identical  ENSMUSG00000038776  113DWRKQVEILNQYPHFKTKI
Ggallus  all identical  ENSGALG00000009291  121NWKKQVEVLNKYPHFKTK
Trubripes  all identical  ENSTRUG00000006133  115DWKKQVAVLNKYPHYKTKIEGLD
Drerio  all identical  ENSDARG00000042854  113NWGKQLDKLNKYPHFKTKI
Dmelanogaster  not conserved  FBgn0034405  122KWSEREEYLKKLDHYQTEIQGLK
Celegans  all conserved  W01A11.1  114DWRKQEATINQFPQFKTEIEGLQ
Xtropicalis  all conserved  ENSXETG00000022654  113NWRKQLDILNKFPHFKTKI
protein features
start (aa)end (aa)featuredetails 
112112CONFLICTR -> K (in Ref. 10).might get lost (downstream of altered splice site)
148148CONFLICTH -> N (in Ref. 3 and 10).might get lost (downstream of altered splice site)
243243CONFLICTV -> L (in Ref. 10).might get lost (downstream of altered splice site)
295295MOD_RESOmega-N-methylated arginine (By similarity).might get lost (downstream of altered splice site)
348348CONFLICTK -> S (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
406406CONFLICTL -> F (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
420420CONFLICTL -> V (in Ref. 3; CAA68486).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1368 / 1368
position (AA) of stopcodon in wt / mu AA sequence 456 / 456
position of stopcodon in wt / mu cDNA 1448 / 1448
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 81 / 81
chromosome 1
strand 1
last intron/exon boundary 1247
theoretical NMD boundary in CDS 1116
length of CDS 1368
coding sequence (CDS) position 337
cDNA position
(for ins/del: last normal base / first normal base)		 417
gDNA position
(for ins/del: last normal base / first normal base)		 21840
chromosomal position
(for ins/del: last normal base / first normal base)		 226019633
original gDNA sequence snippet AGGTGGAGATTCTCAACAGATACCCTCACTTCAAGACTAAG
altered gDNA sequence snippet AGGTGGAGATTCTCAACAGACACCCTCACTTCAAGACTAAG
original cDNA sequence snippet AGGTGGAGATTCTCAACAGATACCCTCACTTCAAGACTAAG
altered cDNA sequence snippet AGGTGGAGATTCTCAACAGACACCCTCACTTCAAGACTAAG
wildtype AA sequence MWLEILLTSV LGFAIYWFIS RDKEETLPLE DGWWGPGTRS AAREDDSIRP FKVETSDEEI
HDLHQRIDKF RFTPPLEDSC FHYGFNSNYL KKVISYWRNE FDWKKQVEIL NRYPHFKTKI
EGLDIHFIHV KPPQLPAGHT PKPLLMVHGW PGSFYEFYKI IPLLTDPKNH GLSDEHVFEV
ICPSIPGYGF SEASSKKGFN SVATARIFYK LMLRLGFQEF YIQGGDWGSL ICTNMAQLVP
SHVKGLHLNM ALVLSNFSTL TLLLGQRFGR FLGLTERDVE LLYPVKEKVF YSLMRESGYM
HIQCTKPDTV GSALNDSPVG LAAYILEKFS TWTNTEFRYL EDGGLERKFS LDDLLTNVML
YWTTGTIISS QRFYKENLGQ GWMTQKHERM KVYVPTGFSA FPFELLHTPE KWVRFKYPKL
ISYSYMVRGG HFAAFEEPEL LAQDIRKFLS VLERQ*
mutated AA sequence MWLEILLTSV LGFAIYWFIS RDKEETLPLE DGWWGPGTRS AAREDDSIRP FKVETSDEEI
HDLHQRIDKF RFTPPLEDSC FHYGFNSNYL KKVISYWRNE FDWKKQVEIL NRHPHFKTKI
EGLDIHFIHV KPPQLPAGHT PKPLLMVHGW PGSFYEFYKI IPLLTDPKNH GLSDEHVFEV
ICPSIPGYGF SEASSKKGFN SVATARIFYK LMLRLGFQEF YIQGGDWGSL ICTNMAQLVP
SHVKGLHLNM ALVLSNFSTL TLLLGQRFGR FLGLTERDVE LLYPVKEKVF YSLMRESGYM
HIQCTKPDTV GSALNDSPVG LAAYILEKFS TWTNTEFRYL EDGGLERKFS LDDLLTNVML
YWTTGTIISS QRFYKENLGQ GWMTQKHERM KVYVPTGFSA FPFELLHTPE KWVRFKYPKL
ISYSYMVRGG HFAAFEEPEL LAQDIRKFLS VLERQ*
speed 0.66 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