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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000370841
Querying Taster for transcript #2: ENST00000370834
Querying Taster for transcript #3: ENST00000420607
Querying Taster for transcript #4: ENST00000541113
Querying Taster for transcript #5: ENST00000543667
MT speed 0 s - this script 6.059694 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACADMdisease_causing_automatic0.999996425687032simple_aaeaffected0I186Tsingle base exchangers121434275show file
ACADMdisease_causing_automatic0.999997343774726simple_aaeaffected0I408Tsingle base exchangers121434275show file
ACADMdisease_causing_automatic0.999997343774726simple_aaeaffected0I379Tsingle base exchangers121434275show file
ACADMdisease_causing_automatic0.999997343774726simple_aaeaffected0I339Tsingle base exchangers121434275show file
ACADMdisease_causing_automatic0.99999972973209simple_aaeaffected0I375Tsingle base exchangers121434275show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999996425687032 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910004)
  • known disease mutation: rs3589 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76226985T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000543667
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.557T>C
cDNA.875T>C
g.36950T>C
AA changes I186T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 186
frameshift no
known variant Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9160.999
4.3771
(flanking)-0.1070.992
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 increased36947wt: 0.8767 / mu: 0.8984 (marginal change - not scored)wt: TGTGCAGATACTTGG
mu: TGTGCAGACACTTGG		 TGCA|gata
Donor gained369420.31mu: GATGCTGTGCAGACA TGCT|gtgc
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      186IANQLATDAVQILGGNGFNTEYPV
mutated  not conserved    186TDAVQTLGGNGFNTEYP
Ptroglodytes  all identical  ENSPTRG00000000871  375TDAVQILGGNGFNTEYP
Mmulatta  all identical  ENSMMUG00000007220  408TDAVQIFGGNGFNTEYP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  375TDAVQIFGGYGFNTEYP
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  404SDAVQVFGGNGFNSEYP
Drerio  all identical  ENSDARG00000038900  380SDAVQIFGGNGFNSEYP
Dmelanogaster  all identical  FBgn0035811  371SDAVQIFGGNGFNSEYP
Celegans  all identical  T08G2.3  365NAVQIFGGNGFNSEYP
Xtropicalis  all conserved  ENSXETG00000002983  380SDAVQVFGGNGFNSDYP
protein features
start (aa)end (aa)featuredetails 
180193STRANDlost
191191MUTAGENW->A: Loss of electron transfer to ETF.might get lost (downstream of altered splice site)
191191MUTAGENW->F: Reduces rate of electron transfer to ETF about six-fold.might get lost (downstream of altered splice site)
191193NP_BINDFAD.might get lost (downstream of altered splice site)
194197TURNmight get lost (downstream of altered splice site)
199206STRANDmight get lost (downstream of altered splice site)
212212MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
215217HELIXmight get lost (downstream of altered splice site)
216216BINDINGSubstrate.might get lost (downstream of altered splice site)
219225STRANDmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
237237MUTAGENE->A: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
239241STRANDmight get lost (downstream of altered splice site)
247258STRANDmight get lost (downstream of altered splice site)
259261HELIXmight get lost (downstream of altered splice site)
262265STRANDmight get lost (downstream of altered splice site)
266268TURNmight get lost (downstream of altered splice site)
269303HELIXmight get lost (downstream of altered splice site)
278281REGIONSubstrate binding.might get lost (downstream of altered splice site)
279279MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
301301MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
306308NP_BINDFAD.might get lost (downstream of altered splice site)
309312STRANDmight get lost (downstream of altered splice site)
313315HELIXmight get lost (downstream of altered splice site)
316317NP_BINDFAD.might get lost (downstream of altered splice site)
317345HELIXmight get lost (downstream of altered splice site)
351376HELIXmight get lost (downstream of altered splice site)
356356CONFLICTI -> T (in Ref. 3; AAF63626).might get lost (downstream of altered splice site)
374378NP_BINDFAD.might get lost (downstream of altered splice site)
377379HELIXmight get lost (downstream of altered splice site)
384384MUTAGENE->A: Reduces rate of electron transfer to ETF three-fold.might get lost (downstream of altered splice site)
384384MUTAGENE->Q: Reduces rate of electron transfer to ETF two-fold.might get lost (downstream of altered splice site)
387394HELIXmight get lost (downstream of altered splice site)
395398HELIXmight get lost (downstream of altered splice site)
399401TURNmight get lost (downstream of altered splice site)
401401ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
402402BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXmight get lost (downstream of altered splice site)
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 699 / 699
position (AA) of stopcodon in wt / mu AA sequence 233 / 233
position of stopcodon in wt / mu cDNA 1017 / 1017
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 319 / 319
chromosome 1
strand 1
last intron/exon boundary 946
theoretical NMD boundary in CDS 577
length of CDS 699
coding sequence (CDS) position 557
cDNA position
(for ins/del: last normal base / first normal base)		 875
gDNA position
(for ins/del: last normal base / first normal base)		 36950
chromosomal position
(for ins/del: last normal base / first normal base)		 76226985
original gDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered gDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
original cDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered cDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
wildtype AA sequence MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
mutated AA sequence MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQTLGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
speed 1.27 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: 0.999997343774726 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910004)
  • known disease mutation: rs3589 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76226985T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000370834
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.1223T>C
cDNA.1302T>C
g.36950T>C
AA changes I408T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 408
frameshift no
known variant Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9160.999
4.3771
(flanking)-0.1070.992
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 increased36947wt: 0.8767 / mu: 0.8984 (marginal change - not scored)wt: TGTGCAGATACTTGG
mu: TGTGCAGACACTTGG		 TGCA|gata
Donor gained369420.31mu: GATGCTGTGCAGACA TGCT|gtgc
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      408IANQLATDAVQILGGNGFNTEYPV
mutated  not conserved    408IANQLATDAVQTLGGNGFNTEYP
Ptroglodytes  all identical  ENSPTRG00000000871  375IANQLATDAVQILGGNGFNTEYP
Mmulatta  all identical  ENSMMUG00000007220  408IANQLATDAVQIFGGNGFNTEYP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  375IANQLATDAVQIFGGYGFNTEYP
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  404IANQVASDAVQVFGGNGFNSEYP
Drerio  all identical  ENSDARG00000038900  380IANQCASDAVQIFGGNGFNSEYP
Dmelanogaster  all identical  FBgn0035811  371MANKIASDAVQIFGGNGFNSEYP
Celegans  all identical  T08G2.3  365ANQAATNAVQIFGGNGFNSEYP
Xtropicalis  all conserved  ENSXETG00000002983  380IANQVASDAVQVFGGNGFNSDYP
protein features
start (aa)end (aa)featuredetails 
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXlost
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1365 / 1365
position (AA) of stopcodon in wt / mu AA sequence 455 / 455
position of stopcodon in wt / mu cDNA 1444 / 1444
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 80 / 80
chromosome 1
strand 1
last intron/exon boundary 1373
theoretical NMD boundary in CDS 1243
length of CDS 1365
coding sequence (CDS) position 1223
cDNA position
(for ins/del: last normal base / first normal base)		 1302
gDNA position
(for ins/del: last normal base / first normal base)		 36950
chromosomal position
(for ins/del: last normal base / first normal base)		 76226985
original gDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered gDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
original cDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered cDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
wildtype AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCDYSVC PLLEACTLYL DAFFLLLTGS
NLNLHLNLGG LGLGTFDACL ISEELAYGCT GVQTAIEGNS LGQMPIIIAG NDQQKKKYLG
RMTEEPLMCA YCVTEPGAGS DVAGIKTKAE KKGDEYIING QKMWITNGGK ANWYFLLARS
DPDPKAPANK AFTGFIVEAD TPGIQIGRKE LNMGQRCSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQILG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
mutated AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCDYSVC PLLEACTLYL DAFFLLLTGS
NLNLHLNLGG LGLGTFDACL ISEELAYGCT GVQTAIEGNS LGQMPIIIAG NDQQKKKYLG
RMTEEPLMCA YCVTEPGAGS DVAGIKTKAE KKGDEYIING QKMWITNGGK ANWYFLLARS
DPDPKAPANK AFTGFIVEAD TPGIQIGRKE LNMGQRCSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQTLG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
speed 0.84 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: 0.999997343774726 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910004)
  • known disease mutation: rs3589 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76226985T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000420607
Genbank transcript ID NM_001127328
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.1136T>C
cDNA.1144T>C
g.36950T>C
AA changes I379T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 379
frameshift no
known variant Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9160.999
4.3771
(flanking)-0.1070.992
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 increased36947wt: 0.8767 / mu: 0.8984 (marginal change - not scored)wt: TGTGCAGATACTTGG
mu: TGTGCAGACACTTGG		 TGCA|gata
Donor gained369420.31mu: GATGCTGTGCAGACA TGCT|gtgc
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      379IANQLATDAVQILGGNGFNTEYPV
mutated  not conserved    379IANQLATDAVQTLGGNGFNTEYP
Ptroglodytes  all identical  ENSPTRG00000000871  375IANQLATDAVQILGGNGFNTEYP
Mmulatta  all identical  ENSMMUG00000007220  408IANQLATDAVQIFGGNGFNT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  375IANQLATDAVQIFGGYGFNTEYP
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  404IANQVASDAVQVFGGNGFNSEYP
Drerio  all identical  ENSDARG00000038900  380IANQCASDAVQIFGGNGFNSEYP
Dmelanogaster  all identical  FBgn0035811  371IASDAVQIFGGNGFNSEYP
Celegans  all identical  T08G2.3  365TANQAATNAVQIFGGNGFNSEYP
Xtropicalis  all conserved  ENSXETG00000002983  380IANQVASDAVQVFGGNGFNSDYP
protein features
start (aa)end (aa)featuredetails 
351376HELIXmight get lost (downstream of altered splice site)
374378NP_BINDFAD.might get lost (downstream of altered splice site)
377379HELIXlost
384384MUTAGENE->Q: Reduces rate of electron transfer to ETF two-fold.might get lost (downstream of altered splice site)
384384MUTAGENE->A: Reduces rate of electron transfer to ETF three-fold.might get lost (downstream of altered splice site)
387394HELIXmight get lost (downstream of altered splice site)
395398HELIXmight get lost (downstream of altered splice site)
399401TURNmight get lost (downstream of altered splice site)
401401ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
402402BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXmight get lost (downstream of altered splice site)
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1278 / 1278
position (AA) of stopcodon in wt / mu AA sequence 426 / 426
position of stopcodon in wt / mu cDNA 1286 / 1286
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 9 / 9
chromosome 1
strand 1
last intron/exon boundary 1215
theoretical NMD boundary in CDS 1156
length of CDS 1278
coding sequence (CDS) position 1136
cDNA position
(for ins/del: last normal base / first normal base)		 1144
gDNA position
(for ins/del: last normal base / first normal base)		 36950
chromosomal position
(for ins/del: last normal base / first normal base)		 76226985
original gDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered gDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
original cDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered cDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
wildtype AA sequence MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
mutated AA sequence MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQTL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
speed 1.01 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: 0.999997343774726 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910004)
  • known disease mutation: rs3589 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76226985T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000541113
Genbank transcript ID N/A
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.1016T>C
cDNA.1069T>C
g.36950T>C
AA changes I339T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 339
frameshift no
known variant Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9160.999
4.3771
(flanking)-0.1070.992
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 increased36947wt: 0.8767 / mu: 0.8984 (marginal change - not scored)wt: TGTGCAGATACTTGG
mu: TGTGCAGACACTTGG		 TGCA|gata
Donor gained369420.31mu: GATGCTGTGCAGACA TGCT|gtgc
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      339IANQLATDAVQILGGNGFNTEYPV
mutated  not conserved    339IANQLATDAVQTLGGNGFNTEYP
Ptroglodytes  all identical  ENSPTRG00000000871  375IANQLATDAVQILGGNGFNTEYP
Mmulatta  all identical  ENSMMUG00000007220  408QLATDAVQIFGGNGFNTEYP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  375IANQLATDAVQIFGGYGFNTEYP
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  404VQVFGGNGFNSEYP
Drerio  all identical  ENSDARG00000038900  380IANQCASDAVQIFGGNGFNSEYP
Dmelanogaster  all identical  FBgn0035811  371MANKIASDAVQIFGGNGFNSEYP
Celegans  all identical  T08G2.3  365TANQAATNAVQIFGGNGFNSEYP
Xtropicalis  all conserved  ENSXETG00000002983  380IANQVASDAVQVFGGNGFNSDYP
protein features
start (aa)end (aa)featuredetails 
317345HELIXlost
351376HELIXmight get lost (downstream of altered splice site)
356356CONFLICTI -> T (in Ref. 3; AAF63626).might get lost (downstream of altered splice site)
374378NP_BINDFAD.might get lost (downstream of altered splice site)
377379HELIXmight get lost (downstream of altered splice site)
384384MUTAGENE->A: Reduces rate of electron transfer to ETF three-fold.might get lost (downstream of altered splice site)
384384MUTAGENE->Q: Reduces rate of electron transfer to ETF two-fold.might get lost (downstream of altered splice site)
387394HELIXmight get lost (downstream of altered splice site)
395398HELIXmight get lost (downstream of altered splice site)
399401TURNmight get lost (downstream of altered splice site)
401401ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
402402BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXmight get lost (downstream of altered splice site)
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1158 / 1158
position (AA) of stopcodon in wt / mu AA sequence 386 / 386
position of stopcodon in wt / mu cDNA 1211 / 1211
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 54 / 54
chromosome 1
strand 1
last intron/exon boundary 1140
theoretical NMD boundary in CDS 1036
length of CDS 1158
coding sequence (CDS) position 1016
cDNA position
(for ins/del: last normal base / first normal base)		 1069
gDNA position
(for ins/del: last normal base / first normal base)		 36950
chromosomal position
(for ins/del: last normal base / first normal base)		 76226985
original gDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered gDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
original cDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered cDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
wildtype AA sequence MLQEFTEQQK EFQATARKFA REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG
GLGLGTFDAC LISEELAYGC TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC
AYCVTEPGAG SDVAGIKTKA EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN
KAFTGFIVEA DTPGIQIGRK ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*
mutated AA sequence MLQEFTEQQK EFQATARKFA REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG
GLGLGTFDAC LISEELAYGC TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC
AYCVTEPGAG SDVAGIKTKA EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN
KAFTGFIVEA DTPGIQIGRK ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQTL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*
speed 0.51 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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999972973209 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910004)
  • known disease mutation: rs3589 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76226985T>CN/A show variant in all transcripts   IGV
HGNC symbol ACADM
Ensembl transcript ID ENST00000370841
Genbank transcript ID NM_000016
UniProt peptide P11310
alteration type single base exchange
alteration region CDS
DNA changes c.1124T>C
cDNA.1561T>C
g.36950T>C
AA changes I375T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 375
frameshift no
known variant Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9160.999
4.3771
(flanking)-0.1070.992
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 increased36947wt: 0.8767 / mu: 0.8984 (marginal change - not scored)wt: TGTGCAGATACTTGG
mu: TGTGCAGACACTTGG		 TGCA|gata
Donor gained369420.31mu: GATGCTGTGCAGACA TGCT|gtgc
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      375IANQLATDAVQILGGNGFNTEYPV
mutated  not conserved    375IANQLATDAVQTLGGNGFNTEYP
Ptroglodytes  all identical  ENSPTRG00000000871  375IANQLATDAVQILGGNGFNTEYP
Mmulatta  all identical  ENSMMUG00000007220  408IANQLATDAVQIFGGNGFNTEYP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  375IANQLATDAVQIFGGYGFNTEYP
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000007137  404IANQVASDAVQVFGGNGFNSEYP
Drerio  all identical  ENSDARG00000038900  380IANQCASDAVQIFGGNGFNSEYP
Dmelanogaster  all identical  FBgn0035811  371SDAVQIFGGNGFNSEYP
Celegans  all identical  T08G2.3  365TANQAATNAVQIFGGNGFNSEYP
Xtropicalis  all conserved  ENSXETG00000002983  380ANQVASDAVQVFGGNGFNSDYP
protein features
start (aa)end (aa)featuredetails 
351376HELIXlost
374378NP_BINDFAD.lost
377379HELIXmight get lost (downstream of altered splice site)
384384MUTAGENE->Q: Reduces rate of electron transfer to ETF two-fold.might get lost (downstream of altered splice site)
384384MUTAGENE->A: Reduces rate of electron transfer to ETF three-fold.might get lost (downstream of altered splice site)
387394HELIXmight get lost (downstream of altered splice site)
395398HELIXmight get lost (downstream of altered splice site)
399401TURNmight get lost (downstream of altered splice site)
401401ACT_SITEProton acceptor.might get lost (downstream of altered splice site)
402402BINDINGSubstrate; via amide nitrogen.might get lost (downstream of altered splice site)
403405NP_BINDFAD.might get lost (downstream of altered splice site)
404417HELIXmight get lost (downstream of altered splice site)
413413BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1266 / 1266
position (AA) of stopcodon in wt / mu AA sequence 422 / 422
position of stopcodon in wt / mu cDNA 1703 / 1703
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 438 / 438
chromosome 1
strand 1
last intron/exon boundary 1632
theoretical NMD boundary in CDS 1144
length of CDS 1266
coding sequence (CDS) position 1124
cDNA position
(for ins/del: last normal base / first normal base)		 1561
gDNA position
(for ins/del: last normal base / first normal base)		 36950
chromosomal position
(for ins/del: last normal base / first normal base)		 76226985
original gDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered gDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
original cDNA sequence snippet AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA
altered cDNA sequence snippet AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA
wildtype AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCGGLGL GTFDACLISE ELAYGCTGVQ
TAIEGNSLGQ MPIIIAGNDQ QKKKYLGRMT EEPLMCAYCV TEPGAGSDVA GIKTKAEKKG
DEYIINGQKM WITNGGKANW YFLLARSDPD PKAPANKAFT GFIVEADTPG IQIGRKELNM
GQRCSDTRGI VFEDVKVPKE NVLIGDGAGF KVAMGAFDKT RPVVAAGAVG LAQRALDEAT
KYALERKTFG KLLVEHQAIS FMLAEMAMKV ELARMSYQRA AWEVDSGRRN TYYASIAKAF
AGDIANQLAT DAVQILGGNG FNTEYPVEKL MRDAKIYQIY EGTSQIQRLI VAREHIDKYK
N*
mutated AA sequence MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI
IPVAAEYDKT GEYPVPLIRR AWELGLMNTH IPENCGGLGL GTFDACLISE ELAYGCTGVQ
TAIEGNSLGQ MPIIIAGNDQ QKKKYLGRMT EEPLMCAYCV TEPGAGSDVA GIKTKAEKKG
DEYIINGQKM WITNGGKANW YFLLARSDPD PKAPANKAFT GFIVEADTPG IQIGRKELNM
GQRCSDTRGI VFEDVKVPKE NVLIGDGAGF KVAMGAFDKT RPVVAAGAVG LAQRALDEAT
KYALERKTFG KLLVEHQAIS FMLAEMAMKV ELARMSYQRA AWEVDSGRRN TYYASIAKAF
AGDIANQLAT DAVQTLGGNG FNTEYPVEKL MRDAKIYQIY EGTSQIQRLI VAREHIDKYK
N*
speed 1.17 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
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Problems