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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000543245
Querying Taster for transcript #2: ENST00000356839
Querying Taster for transcript #3: ENST00000350303
MT speed 0 s - this script 3.763149 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACADVLdisease_causing_automatic0.999999972904684simple_aae0F481Lsingle base exchangers118204017show file
ACADVLdisease_causing_automatic0.999999972904684simple_aae0F458Lsingle base exchangers118204017show file
ACADVLdisease_causing_automatic0.999999997243089simple_aae0F436Lsingle base exchangers118204017show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999972904684 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980012)
  • known disease mutation: rs1632 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127326T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADVL
Ensembl transcript ID ENST00000543245
Genbank transcript ID NM_001270447
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1441T>C
cDNA.1462T>C
g.6883T>C
AA changes F481L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 481
frameshift no
known variant Reference ID: rs118204017
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1632 (pathogenic for Very long chain acyl-CoA dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.8951
(flanking)3.8951
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      481GVERVLRDLRIFRIFEGTNDILRL
mutated  not conserved    481LRIFEGTNDILR
Ptroglodytes  all identical  ENSPTRG00000008664  481GVERVLRDLRVFRIF
Mmulatta  all identical  ENSMMUG00000010538  479GVERVLRDLRIFRIFEGTNDILR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  459GVERVLRDIRIFRIFEGANDILR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  460GVERVMRDLRIFRIFEGTNDILR
Drerio  all identical  ENSDARG00000016687  463DLRIFRIFEGTNDILR
Dmelanogaster  all identical  FBgn0034432  431GLERVLRDLRIFRIFEGTNDILR
Celegans  all identical  E04F6.5  426GLERVLRDLRIFRIFEGANDVLR
Xtropicalis  not conserved  ENSXETG00000031271  255--NRCICSLHCCGLIPWAINPFL-
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
465485HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2037 / 2037
position (AA) of stopcodon in wt / mu AA sequence 679 / 679
position of stopcodon in wt / mu cDNA 2058 / 2058
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 22 / 22
chromosome 17
strand 1
last intron/exon boundary 1918
theoretical NMD boundary in CDS 1846
length of CDS 2037
coding sequence (CDS) position 1441
cDNA position
(for ins/del: last normal base / first normal base)		 1462
gDNA position
(for ins/del: last normal base / first normal base)		 6883
chromosomal position
(for ins/del: last normal base / first normal base)		 7127326
original gDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered gDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
original cDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered cDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
wildtype AA sequence MLGGLAAAAG TRIMGKEIEA EAQRPLRQTW RPGQPPAMTA KTMSSRLTAL LGQPRPGPAR
RPYAGGAAQL ALDKSDSHPS DALTRKKPAK AESKSFAVGM FKGQLTTDQV FPYPSVLNEE
QTQFLKELVE PVSRFFEEVN DPAKNDALEM VEETTWQGLK ELGAFGLQVP SELGGVGLCN
TQYARLVEIV GMHDLGVGIT LGAHQSIGFK GILLFGTKAQ KEKYLPKLAS GETVAAFCLT
EPSSGSDAAS IRTSAVPSPC GKYYTLNGSK LWISNGGLAD IFTVFAKTPV TDPATGAVKE
KITAFVVERG FGGITHGPPE KKMGIKASNT AEVFFDGVRV PSENVLGEVG SGFKVAMHIL
NNGRFGMAAA LAGTMRGIIA KAVDHATNRT QFGEKIHNFG LIQEKLARMV MLQYVTESMA
YMVSANMDQG ATDFQIEAAI SKIFGSEAAW KVTDECIQIM GGMGFMKEPG VERVLRDLRI
FRIFEGTNDI LRLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
mutated AA sequence MLGGLAAAAG TRIMGKEIEA EAQRPLRQTW RPGQPPAMTA KTMSSRLTAL LGQPRPGPAR
RPYAGGAAQL ALDKSDSHPS DALTRKKPAK AESKSFAVGM FKGQLTTDQV FPYPSVLNEE
QTQFLKELVE PVSRFFEEVN DPAKNDALEM VEETTWQGLK ELGAFGLQVP SELGGVGLCN
TQYARLVEIV GMHDLGVGIT LGAHQSIGFK GILLFGTKAQ KEKYLPKLAS GETVAAFCLT
EPSSGSDAAS IRTSAVPSPC GKYYTLNGSK LWISNGGLAD IFTVFAKTPV TDPATGAVKE
KITAFVVERG FGGITHGPPE KKMGIKASNT AEVFFDGVRV PSENVLGEVG SGFKVAMHIL
NNGRFGMAAA LAGTMRGIIA KAVDHATNRT QFGEKIHNFG LIQEKLARMV MLQYVTESMA
YMVSANMDQG ATDFQIEAAI SKIFGSEAAW KVTDECIQIM GGMGFMKEPG VERVLRDLRI
LRIFEGTNDI LRLFVALQGC MDKGKELSGL GSALKNPFGN AGLLLGEAGK QLRRRAGLGS
GLSLSGLVHP ELSRSGELAV RALEQFATVV EAKLIKHKKG IVNEQFLLQR LADGAIDLYA
MVVVLSRASR SLSEGHPTAQ HEKMLCDTWC IEAAARIREG MAALQSDPWQ QELYRNFKSI
SKALVERGGV VTSNPLGF*
speed 0.86 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: 0.999999972904684 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980012)
  • known disease mutation: rs1632 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127326T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADVL
Ensembl transcript ID ENST00000356839
Genbank transcript ID NM_000018
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1372T>C
cDNA.1551T>C
g.6883T>C
AA changes F458L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 458
frameshift no
known variant Reference ID: rs118204017
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1632 (pathogenic for Very long chain acyl-CoA dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.8951
(flanking)3.8951
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      458GVERVLRDLRIFRIFEGTNDILRL
mutated  not conserved    458GVERVLRDLRILRIFEGTNDILR
Ptroglodytes  all identical  ENSPTRG00000008664  481GVERVLRDLRVFRIFEGTNDILR
Mmulatta  all identical  ENSMMUG00000010538  478GVERVLRDLRIF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  459GVERVLRDIRIFRIFEGANDILR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  460GVERVMRDLRIFRIFEGTNDILR
Drerio  all identical  ENSDARG00000016687  463DLRIFRIFEGTNDILR
Dmelanogaster  all identical  FBgn0034432  431GLERVLRDLRIFRIFEGTNDILR
Celegans  all identical  E04F6.5  426GLERVLRDLRIFRIFEGANDVLR
Xtropicalis  not conserved  ENSXETG00000031271  255--NRCICSLHCCGLIPWAINPFL-
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
456459HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1968 / 1968
position (AA) of stopcodon in wt / mu AA sequence 656 / 656
position of stopcodon in wt / mu cDNA 2147 / 2147
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 180 / 180
chromosome 17
strand 1
last intron/exon boundary 2007
theoretical NMD boundary in CDS 1777
length of CDS 1968
coding sequence (CDS) position 1372
cDNA position
(for ins/del: last normal base / first normal base)		 1551
gDNA position
(for ins/del: last normal base / first normal base)		 6883
chromosomal position
(for ins/del: last normal base / first normal base)		 7127326
original gDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered gDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
original cDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered cDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
wildtype AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
mutated AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRILRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*
speed 0.86 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: 0.999999997243089 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980012)
  • known disease mutation: rs1632 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:7127326T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADVL
Ensembl transcript ID ENST00000350303
Genbank transcript ID NM_001033859
UniProt peptide P49748
alteration type single base exchange
alteration region CDS
DNA changes c.1306T>C
cDNA.1428T>C
g.6883T>C
AA changes F436L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 436
frameshift no
known variant Reference ID: rs118204017
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1632 (pathogenic for Very long chain acyl-CoA dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980012)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.8951
(flanking)3.8951
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      436GVERVLRDLRIFRIFEGTNDILRL
mutated  not conserved    436GVERVLRDLRILRIFEGTNDILR
Ptroglodytes  all identical  ENSPTRG00000008664  481GVERVLRDLRVFRIFEGTNDILR
Mmulatta  all identical  ENSMMUG00000010538  478GVERVLRDLRIF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000018574  459GVERVLRDIRIFRIFEGANDILR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000013710  460GVERVMRDLRIFRIFEGTNDILR
Drerio  all identical  ENSDARG00000016687  463GVERVLRDLRIFRIFEGTNDILR
Dmelanogaster  all identical  FBgn0034432  431GLERVLRDLRIFRIFEGTNDILR
Celegans  all identical  E04F6.5  426GLERVLRDLRIFRIFEGANDVLR
Xtropicalis  not conserved  ENSXETG00000031271  255--NRCICSLHCCGLIPWAINPFL-
protein features
start (aa)end (aa)featuredetails 
41482REGIONCatalytic.lost
412437HELIXlost
435439NP_BINDFAD (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1902 / 1902
position (AA) of stopcodon in wt / mu AA sequence 634 / 634
position of stopcodon in wt / mu cDNA 2024 / 2024
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 123 / 123
chromosome 17
strand 1
last intron/exon boundary 1884
theoretical NMD boundary in CDS 1711
length of CDS 1902
coding sequence (CDS) position 1306
cDNA position
(for ins/del: last normal base / first normal base)		 1428
gDNA position
(for ins/del: last normal base / first normal base)		 6883
chromosomal position
(for ins/del: last normal base / first normal base)		 7127326
original gDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered gDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
original cDNA sequence snippet TGCTCCGAGATCTTCGCATCTTCCGGATCTTTGAGGGGACA
altered cDNA sequence snippet TGCTCCGAGATCTTCGCATCCTCCGGATCTTTGAGGGGACA
wildtype AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQESKS FAVGMFKGQL
TTDQVFPYPS VLNEEQTQFL KELVEPVSRF FEEVNDPAKN DALEMVEETT WQGLKELGAF
GLQVPSELGG VGLCNTQYAR LVEIVGMHDL GVGITLGAHQ SIGFKGILLF GTKAQKEKYL
PKLASGETVA AFCLTEPSSG SDAASIRTSA VPSPCGKYYT LNGSKLWISN GGLADIFTVF
AKTPVTDPAT GAVKEKITAF VVERGFGGIT HGPPEKKMGI KASNTAEVFF DGVRVPSENV
LGEVGSGFKV AMHILNNGRF GMAAALAGTM RGIIAKAVDH ATNRTQFGEK IHNFGLIQEK
LARMVMLQYV TESMAYMVSA NMDQGATDFQ IEAAISKIFG SEAAWKVTDE CIQIMGGMGF
MKEPGVERVL RDLRIFRIFE GTNDILRLFV ALQGCMDKGK ELSGLGSALK NPFGNAGLLL
GEAGKQLRRR AGLGSGLSLS GLVHPELSRS GELAVRALEQ FATVVEAKLI KHKKGIVNEQ
FLLQRLADGA IDLYAMVVVL SRASRSLSEG HPTAQHEKML CDTWCIEAAA RIREGMAALQ
SDPWQQELYR NFKSISKALV ERGGVVTSNP LGF*
mutated AA sequence MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQESKS FAVGMFKGQL
TTDQVFPYPS VLNEEQTQFL KELVEPVSRF FEEVNDPAKN DALEMVEETT WQGLKELGAF
GLQVPSELGG VGLCNTQYAR LVEIVGMHDL GVGITLGAHQ SIGFKGILLF GTKAQKEKYL
PKLASGETVA AFCLTEPSSG SDAASIRTSA VPSPCGKYYT LNGSKLWISN GGLADIFTVF
AKTPVTDPAT GAVKEKITAF VVERGFGGIT HGPPEKKMGI KASNTAEVFF DGVRVPSENV
LGEVGSGFKV AMHILNNGRF GMAAALAGTM RGIIAKAVDH ATNRTQFGEK IHNFGLIQEK
LARMVMLQYV TESMAYMVSA NMDQGATDFQ IEAAISKIFG SEAAWKVTDE CIQIMGGMGF
MKEPGVERVL RDLRILRIFE GTNDILRLFV ALQGCMDKGK ELSGLGSALK NPFGNAGLLL
GEAGKQLRRR AGLGSGLSLS GLVHPELSRS GELAVRALEQ FATVVEAKLI KHKKGIVNEQ
FLLQRLADGA IDLYAMVVVL SRASRSLSEG HPTAQHEKML CDTWCIEAAA RIREGMAALQ
SDPWQQELYR NFKSISKALV ERGGVVTSNP LGF*
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

Problems