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 3.90875 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACADMdisease_causing_automatic0.999999999999967simple_aae0C244Rsingle base exchangers121434276show file
ACADMdisease_causing_automatic0.999999999999967simple_aae0C208Rsingle base exchangers121434276show file
ACADMdisease_causing_automatic0.999999999999993simple_aae0C248Rsingle base exchangers121434276show file
ACADMdisease_causing_automatic0.999999999999995simple_aae0C277Rsingle base exchangers121434276show file
ACADMdisease_causing_automatic0.999999999999995simple_aae0C55Rsingle base exchangers121434276show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999967 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>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.730T>C
cDNA.1167T>C
g.25090T>C
AA changes C244R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 244
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (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 CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      244IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    244GQRRSDTRGIVFEDV
Ptroglodytes  all identical  ENSPTRG00000000871  244GQRCSDTRGIVFEDV
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSDTRGIVFEDV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244GQRCSDTRGIAFEDV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRGITFEDV
Drerio  all identical  ENSDARG00000038900  249PGRKELNMGQRCSDTRGITFEDV
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDTRG
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVITFEDV
Xtropicalis  all identical  ENSXETG00000002983  249IGRKEMNMGQRCSDTRGIVFEDV
protein features no protein features affected
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 730
cDNA position
(for ins/del: last normal base / first normal base)		 1167
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
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
GQRRSDTRGI VFEDVKVPKE NVLIGDGAGF KVAMGAFDKT RPVVAAGAVG LAQRALDEAT
KYALERKTFG KLLVEHQAIS FMLAEMAMKV ELARMSYQRA AWEVDSGRRN TYYASIAKAF
AGDIANQLAT DAVQILGGNG FNTEYPVEKL MRDAKIYQIY EGTSQIQRLI VAREHIDKYK
N*
speed 0.53 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: 0.999999999999967 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>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.622T>C
cDNA.675T>C
g.25090T>C
AA changes C208R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 208
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (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 CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      208IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    208IGRKELNMGQRRSDTRGIVFEDV
Ptroglodytes  all identical  ENSPTRG00000000871  244IGRKELNMGQRCSDTRGIVFEDV
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244IGKKELNMGQRCSDTRGIAFEDV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRGITF
Drerio  all identical  ENSDARG00000038900  249PGRKELNMGQRCSDTRGITFEDV
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDTRGITFEDV
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVITFEDV
Xtropicalis  all identical  ENSXETG00000002983  249IGRKEMNMGQRCSDTRGIVFEDV
protein features no protein features affected
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 622
cDNA position
(for ins/del: last normal base / first normal base)		 675
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
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 ELNMGQRRSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*
speed 0.80 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: 0.999999999999993 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>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.742T>C
cDNA.750T>C
g.25090T>C
AA changes C248R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 248
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (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 CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      248IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    248ELNMGQRRSDTRGIVFEDV
Ptroglodytes  all identical  ENSPTRG00000000871  244ELNMGQRCSDTRGIVFEDV
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSDTRGIVFEDV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244ELNMGQRCSDTRGIAFEDV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRGITFEDV
Drerio  all identical  ENSDARG00000038900  249PGRKELNMGQRCSDTRGITFEDV
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDT
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVITFEDV
Xtropicalis  all identical  ENSXETG00000002983  249RCSDTRGIVFEDV
protein features
start (aa)end (aa)featuredetails 
247258STRANDlost
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 742
cDNA position
(for ins/del: last normal base / first normal base)		 750
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
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
ELNMGQRRSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN*
speed 0.58 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: 0.999999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>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.829T>C
cDNA.908T>C
g.25090T>C
AA changes C277R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 277
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (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 CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      277IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    277IGRKELNMGQRRSDTRGIVFEDV
Ptroglodytes  all identical  ENSPTRG00000000871  244IGRKELNMGQRCSDTRGIVFEDV
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSDTRGIVFEDV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244IGKKELNMGQRCSDTRGIAFEDV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRGITFEDV
Drerio  all identical  ENSDARG00000038900  249RCSDTRGITFEDV
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDTRGITFEDV
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVITFEDV
Xtropicalis  all identical  ENSXETG00000002983  249IGRKEMNMGQRCSDTRGIVFEDV
protein features
start (aa)end (aa)featuredetails 
269303HELIXlost
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 829
cDNA position
(for ins/del: last normal base / first normal base)		 908
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
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 LNMGQRRSDT RGIVFEDVKV PKENVLIGDG
AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AISFMLAEMA
MKVELARMSY QRAAWEVDSG RRNTYYASIA KAFAGDIANQ LATDAVQILG GNGFNTEYPV
EKLMRDAKIY QIYEGTSQIQ RLIVAREHID KYKN*
speed 0.61 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: 0.999999999999995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910002)
  • known disease mutation: rs3590 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:76215125T>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.163T>C
cDNA.481T>C
g.25090T>C
AA changes C55R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 55
frameshift no
known variant Reference ID: rs121434276
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3590 (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 CM910002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910002)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3830.907
5.1021
(flanking)6.181
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 increased25085wt: 0.9982 / mu: 0.9986 (marginal change - not scored)wt: GGGCCAGCGATGTTC
mu: GGGCCAGCGACGTTC		 GCCA|gcga
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      55IGRKELNMGQRCSDTRGIVFEDVK
mutated  not conserved    55IGRKELNMGQRRSDTRG
Ptroglodytes  all identical  ENSPTRG00000000871  244IGRKELNMGQRCSDTRG
Mmulatta  all identical  ENSMMUG00000007220  277IGRKELNMGQRCSDTRG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000062908  244IGKKELNMGQRCSDTRG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007137  273IGRKELNMGQRCSDTRG
Drerio  all identical  ENSDARG00000038900  249PGRKELNMGQRCSDTRG
Dmelanogaster  not conserved  FBgn0035811  240PGRKELNMGQRASDTRG
Celegans  all identical  T08G2.3  234RGKKEKNMGQRCSDTRVI
Xtropicalis  all identical  ENSXETG00000002983  249IGRKEMNMGQRCSDTRG
protein features
start (aa)end (aa)featuredetails 
4359HELIXlost
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 163
cDNA position
(for ins/del: last normal base / first normal base)		 481
gDNA position
(for ins/del: last normal base / first normal base)		 25090
chromosomal position
(for ins/del: last normal base / first normal base)		 76215125
original gDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered gDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
original cDNA sequence snippet AATTAAACATGGGCCAGCGATGTTCAGATACTAGAGGAATT
altered cDNA sequence snippet AATTAAACATGGGCCAGCGACGTTCAGATACTAGAGGAATT
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 MGQRRSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*
speed 0.63 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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