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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 4.679487 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACADMdisease_causing0.999999995914617simple_aaeaffectedT4Asingle base exchangers121434279show file
ACADMdisease_causing0.999999998501088simple_aaeaffectedT226Asingle base exchangers121434279show file
ACADMdisease_causing0.999999999669047simple_aaeaffectedT157Asingle base exchangers121434279show file
ACADMdisease_causing0.999999999703457simple_aaeaffectedT197Asingle base exchangers121434279show file
ACADMdisease_causing0.999999999966326simple_aaeaffectedT193Asingle base exchangers121434279show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995914617      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3595 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970026)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76205773A>GN/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.10A>G
cDNA.328A>G
g.15738A>G
AA changes T4A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 4
frameshift no
known variant Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable 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 CM970026)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3681
4.941
(flanking)5.9841
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 increased15741wt: 0.8986 / mu: 0.9181 (marginal change - not scored)wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA		 ACCA|acgg
Donor gained157370.70mu: TGGATAGCCAACGGA GATA|gcca
Donor gained157320.40mu: AGATGTGGATAGCCA ATGT|ggat
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      4 MWITNGGKANWYFLLA
mutated  not conserved    4 MWIANGGKANWYFLLARSDPDP
Ptroglodytes  all identical  ENSPTRG00000000871  193 MWITNGGKANWYFLLARSDPDP
Mmulatta  all identical  ENSMMUG00000007220  226 MWITNGGKASWYFLLARSDPDP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  193 MWITNGGKANWYFLLARSNPDP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  222 MWITNGGKANWYFLLARTNPDP
Drerio  all identical  ENSDARG00000038900  198 MWITNGGKANWYFLLARTDSDP
Dmelanogaster  all identical  FBgn0035811  189 MWITNGGVANWYFVLARTNPDP
Celegans  all identical  T08G2.3  183 WITGGGHAKWFFVLARSDPNP
Xtropicalis  all identical  ENSXETG00000002983  198 MWITNGGKANWYFLLARTNPDP
protein features
start (aa)end (aa)featuredetails 
125TRANSITMitochondrion.lost
3638STRANDmight get lost (downstream of altered splice site)
4359HELIXmight get lost (downstream of altered splice site)
6170HELIXmight get lost (downstream of altered splice site)
7584HELIXmight get lost (downstream of altered splice site)
8686MUTAGENL->M: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
9395HELIXmight get lost (downstream of altered splice site)
9898MUTAGENL->W: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
100100MUTAGENL->Y: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
102115HELIXmight get lost (downstream of altered splice site)
108108MUTAGENI->M: Strongly reduced rate of electron transfer to ETF.might get lost (downstream of altered splice site)
117129HELIXmight get lost (downstream of altered splice site)
131136HELIXmight get lost (downstream of altered splice site)
139151HELIXmight get lost (downstream of altered splice site)
156159STRANDmight get lost (downstream of altered splice site)
158167NP_BINDFAD.might get lost (downstream of altered splice site)
165168STRANDmight get lost (downstream of altered splice site)
167167BINDINGSubstrate; via carbonyl oxygen.might get lost (downstream of altered splice site)
169171HELIXmight get lost (downstream of altered splice site)
175178STRANDmight get lost (downstream of altered splice site)
180193STRANDmight get lost (downstream of altered splice site)
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->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 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 10
cDNA position
(for ins/del: last normal base / first normal base)		 328
gDNA position
(for ins/del: last normal base / first normal base)		 15738
chromosomal position
(for ins/del: last normal base / first normal base)		 76205773
original gDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered gDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
original cDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered cDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
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 MWIANGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
speed 0.49 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: 0.999999998501088      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3595 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970026)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76205773A>GN/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.676A>G
cDNA.755A>G
g.15738A>G
AA changes T226A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 226
frameshift no
known variant Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable 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 CM970026)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3681
4.941
(flanking)5.9841
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 increased15741wt: 0.8986 / mu: 0.9181 (marginal change - not scored)wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA		 ACCA|acgg
Donor gained157370.70mu: TGGATAGCCAACGGA GATA|gcca
Donor gained157320.40mu: AGATGTGGATAGCCA ATGT|ggat
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      226EYIINGQKMWITNGGKANWYFLLA
mutated  not conserved    226EYIINGQKMWIANGGKANWYFLL
Ptroglodytes  all identical  ENSPTRG00000000871  193EYIINGQKMWITNGGKANWYFLL
Mmulatta  all identical  ENSMMUG00000007220  226EYIINGQKMWITNGGKASWYFLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  193EYVINGQKMWITNGGKANWYFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  222EYVVNGQKMWITNGGKANWYFLL
Drerio  all identical  ENSDARG00000038900  198YVINGQKMWITNGGKANWYFLL
Dmelanogaster  all identical  FBgn0035811  189EWVINGQKMWITNGGVANWYFVL
Celegans  all identical  T08G2.3  183INGSKAWITGGGHAKWFFVL
Xtropicalis  all identical  ENSXETG00000002983  198EYIINGQKMWITNGGKANWYFLL
protein features
start (aa)end (aa)featuredetails 
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 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 676
cDNA position
(for ins/del: last normal base / first normal base)		 755
gDNA position
(for ins/del: last normal base / first normal base)		 15738
chromosomal position
(for ins/del: last normal base / first normal base)		 76205773
original gDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered gDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
original cDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered cDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
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 QKMWIANGGK ANWYFLLARS
DPDPKAPANK AFTGFIVEAD TPGIQIGRKE LNMGQRCSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQILG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
speed 0.46 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: 0.999999999669047      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3595 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970026)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76205773A>GN/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.469A>G
cDNA.522A>G
g.15738A>G
AA changes T157A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable 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 CM970026)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3681
4.941
(flanking)5.9841
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 increased15741wt: 0.8986 / mu: 0.9181 (marginal change - not scored)wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA		 ACCA|acgg
Donor gained157370.70mu: TGGATAGCCAACGGA GATA|gcca
Donor gained157320.40mu: AGATGTGGATAGCCA ATGT|ggat
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157EYIINGQKMWITNGGKANWYFLLA
mutated  not conserved    157EYIINGQKMWIANGGKANWYFLL
Ptroglodytes  all identical  ENSPTRG00000000871  193EYIINGQKMWITNGGKANWYFLL
Mmulatta  all identical  ENSMMUG00000007220  226GQKMWITNGGKASWYFLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  193EYVINGQKMWITNGGKANWYFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  222TNGGKANWYFLL
Drerio  all identical  ENSDARG00000038900  198DYVINGQKMWITNGGKANWYFLL
Dmelanogaster  all identical  FBgn0035811  189EWVINGQKMWITNGGVANWYFVL
Celegans  all identical  T08G2.3  183EYIINGSKAWITGGGHAKWFFVL
Xtropicalis  all identical  ENSXETG00000002983  198EYIINGQKMWITNGGKANWYFLL
protein features
start (aa)end (aa)featuredetails 
156159STRANDlost
158167NP_BINDFAD.might get lost (downstream of altered splice site)
165168STRANDmight get lost (downstream of altered splice site)
167167BINDINGSubstrate; via carbonyl oxygen.might get lost (downstream of altered splice site)
169171HELIXmight get lost (downstream of altered splice site)
175178STRANDmight get lost (downstream of altered splice site)
180193STRANDmight 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)
191191MUTAGENW->A: Loss of electron transfer to ETF.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->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 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 469
cDNA position
(for ins/del: last normal base / first normal base)		 522
gDNA position
(for ins/del: last normal base / first normal base)		 15738
chromosomal position
(for ins/del: last normal base / first normal base)		 76205773
original gDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered gDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
original cDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered cDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
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 GQKMWIANGG KANWYFLLAR SDPDPKAPAN
KAFTGFIVEA DTPGIQIGRK ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*
speed 1.11 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: 0.999999999703457      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3595 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970026)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76205773A>GN/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.589A>G
cDNA.597A>G
g.15738A>G
AA changes T197A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 197
frameshift no
known variant Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable 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 CM970026)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3681
4.941
(flanking)5.9841
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 increased15741wt: 0.8986 / mu: 0.9181 (marginal change - not scored)wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA		 ACCA|acgg
Donor gained157370.70mu: TGGATAGCCAACGGA GATA|gcca
Donor gained157320.40mu: AGATGTGGATAGCCA ATGT|ggat
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      197EYIINGQKMWITNGGKANWYFLLA
mutated  not conserved    197EYIINGQKMWIANGGKANWYFLL
Ptroglodytes  all identical  ENSPTRG00000000871  193EYIINGQKMWITNGGKANWYFLL
Mmulatta  all identical  ENSMMUG00000007220  226EYIINGQKMWITNGGKASWYFL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  193EYVINGQKMWITNGGKANWYFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  222EYVVNGQKMWITNGGKANWYFLL
Drerio  all identical  ENSDARG00000038900  198DYVINGQKMWITNGGKANWYFLL
Dmelanogaster  all identical  FBgn0035811  189QKMWITNGGVANWYFVL
Celegans  all identical  T08G2.3  183EYIINGSKAWITGGGHAKWFFVL
Xtropicalis  all identical  ENSXETG00000002983  198YIINGQKMWITNGGKANWYFLL
protein features
start (aa)end (aa)featuredetails 
194197TURNlost
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 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 589
cDNA position
(for ins/del: last normal base / first normal base)		 597
gDNA position
(for ins/del: last normal base / first normal base)		 15738
chromosomal position
(for ins/del: last normal base / first normal base)		 76205773
original gDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered gDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
original cDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered cDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
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 GQKMWIANGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
speed 1.08 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: 0.999999999966326      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3595 (probable pathogenic)
  • known disease mutation at this position (HGMD CM970026)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76205773A>GN/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.577A>G
cDNA.1014A>G
g.15738A>G
AA changes T193A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 193
frameshift no
known variant Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable 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 CM970026)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3681
4.941
(flanking)5.9841
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 increased15741wt: 0.8986 / mu: 0.9181 (marginal change - not scored)wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA		 ACCA|acgg
Donor gained157370.70mu: TGGATAGCCAACGGA GATA|gcca
Donor gained157320.40mu: AGATGTGGATAGCCA ATGT|ggat
distance from splice site 23
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      193EYIINGQKMWITNGGKANWYFLLA
mutated  not conserved    193EYIINGQKMWIANGGKANWYFLL
Ptroglodytes  all identical  ENSPTRG00000000871  193EYIINGQKMWITNGGKANWYFLL
Mmulatta  all identical  ENSMMUG00000007220  226EYIINGQKMWITNGGKASWYFLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  193EYVINGQKMWITNGGKANWYFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  222EYVVNGQKMWITNGGKANWYFLL
Drerio  all identical  ENSDARG00000038900  198DYVINGQKMWITNGGKANWYFLL
Dmelanogaster  all identical  FBgn0035811  189MWITNGGVANWYFVL
Celegans  all identical  T08G2.3  183EYIINGSKAWITGGGHAKWFFVL
Xtropicalis  all identical  ENSXETG00000002983  198INGQKMWITNGGKANWYFLL
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.lost
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 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 577
cDNA position
(for ins/del: last normal base / first normal base)		 1014
gDNA position
(for ins/del: last normal base / first normal base)		 15738
chromosomal position
(for ins/del: last normal base / first normal base)		 76205773
original gDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered gDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
original cDNA sequence snippet ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT
altered cDNA sequence snippet ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT
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 WIANGGKANW YFLLARSDPD PKAPANKAFT GFIVEADTPG IQIGRKELNM
GQRCSDTRGI VFEDVKVPKE NVLIGDGAGF KVAMGAFDKT RPVVAAGAVG LAQRALDEAT
KYALERKTFG KLLVEHQAIS FMLAEMAMKV ELARMSYQRA AWEVDSGRRN TYYASIAKAF
AGDIANQLAT DAVQILGGNG FNTEYPVEKL MRDAKIYQIY EGTSQIQRLI VAREHIDKYK
N*
speed 0.43 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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