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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000540367
Querying Taster for transcript #2: ENST00000539743
Querying Taster for transcript #3: ENST00000376618
Querying Taster for transcript #4: ENST00000265641
MT speed 4.65 s - this script 5.43586 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CPT1Adisease_causing_automatic0.999999999797932simple_aae0D454Gsingle base exchangers80356778show file
CPT1Adisease_causing_automatic0.999999999797932simple_aae0D454Gsingle base exchangers80356778show file
CPT1Adisease_causing_automatic0.999999999797932simple_aae0D454Gsingle base exchangers80356778show file
CPT1Adisease_causing_automatic0.999999999797932simple_aae0D454Gsingle base exchangers80356778show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999797932 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983369)
  • known disease mutation: rs9061 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:68548205T>CN/A show variant in all transcripts   IGV
HGNC symbol CPT1A
Ensembl transcript ID ENST00000540367
Genbank transcript ID N/A
UniProt peptide P50416
alteration type single base exchange
alteration region CDS
DNA changes c.1361A>G
cDNA.1390A>G
g.63674A>G
AA changes D454G Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 454
frameshift no
known variant Reference ID: rs80356778
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9061 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5041
4.8471
(flanking)5.8671
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased63665wt: 0.5900 / mu: 0.6452 (marginal change - not scored)wt: ACACATGTGTGTTTCACGTAGGTGGTTTGACAAGTCGTTCA
mu: ACACATGTGTGTTTCACGTAGGTGGTTTGGCAAGTCGTTCA		 gtag|GTGG
Donor marginally increased63672wt: 0.9936 / mu: 0.9939 (marginal change - not scored)wt: TGGTTTGACAAGTCG
mu: TGGTTTGGCAAGTCG		 GTTT|gaca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      454LLHGRCYDRWFDKSFTFVVFKNGK
mutated  not conserved    454LLHGRCYDRWFGKSFTFVVFKNG
Ptroglodytes  all identical  ENSPTRG00000003987  454LLHGRCYDRWFDKSFTFVVFKNG
Mmulatta  all identical  ENSMMUG00000001780  454LLHGQCYDRWFDKSFTFVVFKNG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024900  454LLHGRCFDRWFDKSITFVVFKNS
Ggallus  all identical  ENSGALG00000007077  454LIHGRCYDRWFDKTFTLVVFKNG
Trubripes  all identical  ENSTRUG00000009681  457LLHGKCYDRWFDKSFNLIVFKNG
Drerio  all identical  ENSDARG00000062054  454LLHGKCYDRWFDKSLNLIVFKNG
Dmelanogaster  all identical  FBgn0261862  453LLHGNGYNRWFDKCFTVCVGTNG
Celegans  all identical  Y46G5A.17  456LLHGKAHDRWFDKSFNLIISKNG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123773TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2271 / 2271
position (AA) of stopcodon in wt / mu AA sequence 757 / 757
position of stopcodon in wt / mu cDNA 2300 / 2300
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 30 / 30
chromosome 11
strand -1
last intron/exon boundary 2265
theoretical NMD boundary in CDS 2185
length of CDS 2271
coding sequence (CDS) position 1361
cDNA position
(for ins/del: last normal base / first normal base)		 1390
gDNA position
(for ins/del: last normal base / first normal base)		 63674
chromosomal position
(for ins/del: last normal base / first normal base)		 68548205
original gDNA sequence snippet TGTTTCACGTAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered gDNA sequence snippet TGTTTCACGTAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
original cDNA sequence snippet ATGTTACGACAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered cDNA sequence snippet ATGTTACGACAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
wildtype AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*
mutated AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFGKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*
speed 1.31 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: 0.999999999797932 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983369)
  • known disease mutation: rs9061 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:68548205T>CN/A show variant in all transcripts   IGV
HGNC symbol CPT1A
Ensembl transcript ID ENST00000539743
Genbank transcript ID N/A
UniProt peptide P50416
alteration type single base exchange
alteration region CDS
DNA changes c.1361A>G
cDNA.1390A>G
g.63674A>G
AA changes D454G Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 454
frameshift no
known variant Reference ID: rs80356778
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9061 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5041
4.8471
(flanking)5.8671
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased63665wt: 0.5900 / mu: 0.6452 (marginal change - not scored)wt: ACACATGTGTGTTTCACGTAGGTGGTTTGACAAGTCGTTCA
mu: ACACATGTGTGTTTCACGTAGGTGGTTTGGCAAGTCGTTCA		 gtag|GTGG
Donor marginally increased63672wt: 0.9936 / mu: 0.9939 (marginal change - not scored)wt: TGGTTTGACAAGTCG
mu: TGGTTTGGCAAGTCG		 GTTT|gaca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      454LLHGRCYDRWFDKSFTFVVFKNGK
mutated  not conserved    454LLHGRCYDRWFGKSFTFVVFKNG
Ptroglodytes  all identical  ENSPTRG00000003987  454LLHGRCYDRWFDKSFTFVVFKNG
Mmulatta  all identical  ENSMMUG00000001780  454LLHGQCYDRWFDKSFTFVVFKNG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024900  454LLHGRCFDRWFDKSITFVVFKNS
Ggallus  all identical  ENSGALG00000007077  454LIHGRCYDRWFDKTFTLVVFKNG
Trubripes  all identical  ENSTRUG00000009681  457LLHGKCYDRWFDKSFNLIVFKNG
Drerio  all identical  ENSDARG00000062054  454LLHGKCYDRWFDKSLNLIVFKNG
Dmelanogaster  all identical  FBgn0261862  453LLHGNGYNRWFDKCFTVCVGTNG
Celegans  all identical  Y46G5A.17  456LLHGKAHDRWFDKSFNLIISKNG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123773TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2322 / 2322
position (AA) of stopcodon in wt / mu AA sequence 774 / 774
position of stopcodon in wt / mu cDNA 2351 / 2351
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 30 / 30
chromosome 11
strand -1
last intron/exon boundary 2265
theoretical NMD boundary in CDS 2185
length of CDS 2322
coding sequence (CDS) position 1361
cDNA position
(for ins/del: last normal base / first normal base)		 1390
gDNA position
(for ins/del: last normal base / first normal base)		 63674
chromosomal position
(for ins/del: last normal base / first normal base)		 68548205
original gDNA sequence snippet TGTTTCACGTAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered gDNA sequence snippet TGTTTCACGTAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
original cDNA sequence snippet ATGTTACGACAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered cDNA sequence snippet ATGTTACGACAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
wildtype AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETDSHRF GRHLKEAMTD IITLFGLSSN SKK*
mutated AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFGKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETDSHRF GRHLKEAMTD IITLFGLSSN SKK*
speed 1.43 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999797932 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983369)
  • known disease mutation: rs9061 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:68548205T>CN/A show variant in all transcripts   IGV
HGNC symbol CPT1A
Ensembl transcript ID ENST00000376618
Genbank transcript ID NM_001031847
UniProt peptide P50416
alteration type single base exchange
alteration region CDS
DNA changes c.1361A>G
cDNA.1531A>G
g.63674A>G
AA changes D454G Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 454
frameshift no
known variant Reference ID: rs80356778
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9061 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5041
4.8471
(flanking)5.8671
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased63665wt: 0.5900 / mu: 0.6452 (marginal change - not scored)wt: ACACATGTGTGTTTCACGTAGGTGGTTTGACAAGTCGTTCA
mu: ACACATGTGTGTTTCACGTAGGTGGTTTGGCAAGTCGTTCA		 gtag|GTGG
Donor marginally increased63672wt: 0.9936 / mu: 0.9939 (marginal change - not scored)wt: TGGTTTGACAAGTCG
mu: TGGTTTGGCAAGTCG		 GTTT|gaca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      454LLHGRCYDRWFDKSFTFVVFKNGK
mutated  not conserved    454LLHGRCYDRWFGKSFTFVVFKNG
Ptroglodytes  all identical  ENSPTRG00000003987  454LLHGRCYDRWFDKSFTFVVFKNG
Mmulatta  all identical  ENSMMUG00000001780  454LLHGQCYDRWFDKSFTFVVFKNG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024900  454LLHGRCFDRWFDKSITFVVFKNS
Ggallus  all identical  ENSGALG00000007077  454LIHGRCYDRWFDKTFTLVVFKNG
Trubripes  all identical  ENSTRUG00000009681  457LLHGKCYDRWFDKSFNLIVFKNG
Drerio  all identical  ENSDARG00000062054  454LLHGKCYDRWFDKSLNLIVFKNG
Dmelanogaster  all identical  FBgn0261862  453LLHGNGYNRWFDKCFTVCVGTNG
Celegans  all identical  Y46G5A.17  456LLHGKAHDRWFDKSFNLIISKNG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123773TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2271 / 2271
position (AA) of stopcodon in wt / mu AA sequence 757 / 757
position of stopcodon in wt / mu cDNA 2441 / 2441
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 171 / 171
chromosome 11
strand -1
last intron/exon boundary 2406
theoretical NMD boundary in CDS 2185
length of CDS 2271
coding sequence (CDS) position 1361
cDNA position
(for ins/del: last normal base / first normal base)		 1531
gDNA position
(for ins/del: last normal base / first normal base)		 63674
chromosomal position
(for ins/del: last normal base / first normal base)		 68548205
original gDNA sequence snippet TGTTTCACGTAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered gDNA sequence snippet TGTTTCACGTAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
original cDNA sequence snippet ATGTTACGACAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered cDNA sequence snippet ATGTTACGACAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
wildtype AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*
mutated AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFGKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*
speed 0.71 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: 0.999999999797932 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983369)
  • known disease mutation: rs9061 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:68548205T>CN/A show variant in all transcripts   IGV
HGNC symbol CPT1A
Ensembl transcript ID ENST00000265641
Genbank transcript ID NM_001876
UniProt peptide P50416
alteration type single base exchange
alteration region CDS
DNA changes c.1361A>G
cDNA.1531A>G
g.63674A>G
AA changes D454G Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 454
frameshift no
known variant Reference ID: rs80356778
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9061 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983369)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5041
4.8471
(flanking)5.8671
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased63665wt: 0.5900 / mu: 0.6452 (marginal change - not scored)wt: ACACATGTGTGTTTCACGTAGGTGGTTTGACAAGTCGTTCA
mu: ACACATGTGTGTTTCACGTAGGTGGTTTGGCAAGTCGTTCA		 gtag|GTGG
Donor marginally increased63672wt: 0.9936 / mu: 0.9939 (marginal change - not scored)wt: TGGTTTGACAAGTCG
mu: TGGTTTGGCAAGTCG		 GTTT|gaca
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      454LLHGRCYDRWFDKSFTFVVFKNGK
mutated  not conserved    454LLHGRCYDRWFGKSFTFVVFKNG
Ptroglodytes  all identical  ENSPTRG00000003987  454LLHGRCYDRWFDKSFTFVVFKNG
Mmulatta  all identical  ENSMMUG00000001780  454LLHGQCYDRWFDKSFTFVVFKNG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000024900  454LLHGRCFDRWFDKSITFVVFKNS
Ggallus  all identical  ENSGALG00000007077  454LIHGRCYDRWFDKTFTLVVFKNG
Trubripes  all identical  ENSTRUG00000009681  457LLHGKCYDRWFDKSFNLIVFKNG
Drerio  all identical  ENSDARG00000062054  454LLHGKCYDRWFDKSLNLIVFKNG
Dmelanogaster  all identical  FBgn0261862  453LLHGNGYNRWFDKCFTVCVGTNG
Celegans  all identical  Y46G5A.17  456LLHGKAHDRWFDKSFNLIISKNG
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123773TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2322 / 2322
position (AA) of stopcodon in wt / mu AA sequence 774 / 774
position of stopcodon in wt / mu cDNA 2492 / 2492
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 171 / 171
chromosome 11
strand -1
last intron/exon boundary 2406
theoretical NMD boundary in CDS 2185
length of CDS 2322
coding sequence (CDS) position 1361
cDNA position
(for ins/del: last normal base / first normal base)		 1531
gDNA position
(for ins/del: last normal base / first normal base)		 63674
chromosomal position
(for ins/del: last normal base / first normal base)		 68548205
original gDNA sequence snippet TGTTTCACGTAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered gDNA sequence snippet TGTTTCACGTAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
original cDNA sequence snippet ATGTTACGACAGGTGGTTTGACAAGTCGTTCACGTTTGTTG
altered cDNA sequence snippet ATGTTACGACAGGTGGTTTGGCAAGTCGTTCACGTTTGTTG
wildtype AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETDSHRF GRHLKEAMTD IITLFGLSSN SKK*
mutated AA sequence MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFGKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETDSHRF GRHLKEAMTD IITLFGLSSN SKK*
speed 1.20 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems