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: ENST00000375320
Querying Taster for transcript #2: ENST00000359492
Querying Taster for transcript #3: ENST00000375329
Querying Taster for transcript #4: ENST00000375323
Querying Taster for transcript #5: ENST00000236850
MT speed 0 s - this script 4.746645 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APOA1disease_causing_automatic0.00175902704440179simple_aaeaffected0L198Ssingle base exchangers121912729show file
APOA1disease_causing_automatic0.00175902704440179simple_aaeaffected0L198Ssingle base exchangers121912729show file
APOA1disease_causing_automatic0.00175902704440179simple_aaeaffected0L176Ssingle base exchangers121912729show file
APOA1disease_causing_automatic0.00175902704440179simple_aaeaffected0L198Ssingle base exchangers121912729show file
APOA1disease_causing_automatic0.00175902704440179simple_aaeaffected0L198Ssingle base exchangers121912729show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.00175902704440179 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993804)
  • known disease mutation: rs17933 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706735A>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000375320
Genbank transcript ID N/A
UniProt peptide P02647
alteration type single base exchange
alteration region CDS
DNA changes c.593T>C
cDNA.672T>C
g.1932T>C
AA changes L198S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs121912729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17933 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7950.124
1.2670.111
(flanking)0.1240.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1933wt: 0.45 / mu: 0.81wt: CGCTTGGCCGCGCGC
mu: CGCTCGGCCGCGCGC		 CTTG|gccg
distance from splice site 269
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198LAPYSDELRQRLAARLEALKENGG
mutated  not conserved    198LAPYSDELRQRSAARLEALKENG
Ptroglodytes  all identical  ENSPTRG00000004316  198LAPYSDELRQRLAARLEALKENG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  197LAPHSEQMRESLAQRLAELKSN-
Ggallus  all identical  ENSGALG00000007114  183RQKLSQKLEEIREKG
Trubripes  all identical  ENSTRUG00000007686  194LMPIVEKVHTKLAEYVEQIKAVV
Drerio  all conserved  ENSDARG00000086583  212LEPYVQEYKDQM--------EKG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  190LTPYSEEVRVKLVEKLEELKANA
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
166203HELIXlost
189210REPEAT7.lost
211232REPEAT8.might get lost (downstream of altered splice site)
212214TURNmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
220237HELIXmight get lost (downstream of altered splice site)
233243REPEAT9; half-length.might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
243266HELIXmight get lost (downstream of altered splice site)
244267REPEAT10.might get lost (downstream of altered splice site)
263263CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 883 / 883
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 11
strand -1
last intron/exon boundary 280
theoretical NMD boundary in CDS 150
length of CDS 804
coding sequence (CDS) position 593
cDNA position
(for ins/del: last normal base / first normal base)		 672
gDNA position
(for ins/del: last normal base / first normal base)		 1932
chromosomal position
(for ins/del: last normal base / first normal base)		 116706735
original gDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered gDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
original cDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered cDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
wildtype AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
mutated AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRSAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.83 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: 0.00175902704440179 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993804)
  • known disease mutation: rs17933 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706735A>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000359492
Genbank transcript ID N/A
UniProt peptide P02647
alteration type single base exchange
alteration region CDS
DNA changes c.593T>C
cDNA.664T>C
g.1932T>C
AA changes L198S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs121912729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17933 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7950.124
1.2670.111
(flanking)0.1240.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1933wt: 0.45 / mu: 0.81wt: CGCTTGGCCGCGCGC
mu: CGCTCGGCCGCGCGC		 CTTG|gccg
distance from splice site 269
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198LAPYSDELRQRLAARLEALKENGG
mutated  not conserved    198LAPYSDELRQRSAARLEALKENG
Ptroglodytes  all identical  ENSPTRG00000004316  198LAPYSDELRQRLAARLEALKENG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  197LAPHSEQMRESLAQRLAELKSN-
Ggallus  all identical  ENSGALG00000007114  183RQKLSQKLEEIREKG
Trubripes  all identical  ENSTRUG00000007686  194LMPIVEKVHTKLAEYVEQIKAVV
Drerio  all conserved  ENSDARG00000086583  212LEPYVQEYKDQM--------EKG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  190LTPYSEEVRVKLVEKLEELKANA
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
166203HELIXlost
189210REPEAT7.lost
211232REPEAT8.might get lost (downstream of altered splice site)
212214TURNmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
220237HELIXmight get lost (downstream of altered splice site)
233243REPEAT9; half-length.might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
243266HELIXmight get lost (downstream of altered splice site)
244267REPEAT10.might get lost (downstream of altered splice site)
263263CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 875 / 875
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 72 / 72
chromosome 11
strand -1
last intron/exon boundary 272
theoretical NMD boundary in CDS 150
length of CDS 804
coding sequence (CDS) position 593
cDNA position
(for ins/del: last normal base / first normal base)		 664
gDNA position
(for ins/del: last normal base / first normal base)		 1932
chromosomal position
(for ins/del: last normal base / first normal base)		 116706735
original gDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered gDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
original cDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered cDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
wildtype AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
mutated AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRSAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.57 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: 0.00175902704440179 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993804)
  • known disease mutation: rs17933 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706735A>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000375329
Genbank transcript ID N/A
UniProt peptide P02647
alteration type single base exchange
alteration region CDS
DNA changes c.527T>C
cDNA.659T>C
g.1932T>C
AA changes L176S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 176
frameshift no
known variant Reference ID: rs121912729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17933 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7950.124
1.2670.111
(flanking)0.1240.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1933wt: 0.45 / mu: 0.81wt: CGCTTGGCCGCGCGC
mu: CGCTCGGCCGCGCGC		 CTTG|gccg
distance from splice site 269
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176LAPYSDELRQRLAARLEALKENGG
mutated  not conserved    176LAPYSDELRQRSAARL
Ptroglodytes  all identical  ENSPTRG00000004316  198LAPYSDELRQRLAARLEALKENG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  197LAPHSEQMRESLAQRLAELKSN-
Ggallus  all identical  ENSGALG00000007114  183APYSDELRQKLSQKLEEIREKG
Trubripes  all identical  ENSTRUG00000007686  216VNEYKEEL
Drerio  all conserved  ENSDARG00000086583  212QM--------EKG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  190LTPYSEEVRVKLVEKLEELKANA
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
166203HELIXlost
167188REPEAT6.lost
189210REPEAT7.might get lost (downstream of altered splice site)
191191MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
211232REPEAT8.might get lost (downstream of altered splice site)
212214TURNmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
220237HELIXmight get lost (downstream of altered splice site)
233243REPEAT9; half-length.might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
243266HELIXmight get lost (downstream of altered splice site)
244267REPEAT10.might get lost (downstream of altered splice site)
263263CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 738 / 738
position (AA) of stopcodon in wt / mu AA sequence 246 / 246
position of stopcodon in wt / mu cDNA 870 / 870
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 133 / 133
chromosome 11
strand -1
last intron/exon boundary 267
theoretical NMD boundary in CDS 84
length of CDS 738
coding sequence (CDS) position 527
cDNA position
(for ins/del: last normal base / first normal base)		 659
gDNA position
(for ins/del: last normal base / first normal base)		 1932
chromosomal position
(for ins/del: last normal base / first normal base)		 116706735
original gDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered gDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
original cDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered cDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
wildtype AA sequence MSGGARGFCM LKAPHSARPF FSSRSPTALQ DESCGADLGR ALPDGLKLLD NWDSVTSTFS
KLREQLGPVT QEFWDNLEKE TEGLRQEMSK DLEEVKAKVQ PYLDDFQKKW QEEMELYRQK
VEPLRAELQE GARQKLHELQ EKLSPLGEEM RDRARAHVDA LRTHLAPYSD ELRQRLAARL
EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK
KLNTQ*
mutated AA sequence MSGGARGFCM LKAPHSARPF FSSRSPTALQ DESCGADLGR ALPDGLKLLD NWDSVTSTFS
KLREQLGPVT QEFWDNLEKE TEGLRQEMSK DLEEVKAKVQ PYLDDFQKKW QEEMELYRQK
VEPLRAELQE GARQKLHELQ EKLSPLGEEM RDRARAHVDA LRTHLAPYSD ELRQRSAARL
EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK
KLNTQ*
speed 0.95 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: 0.00175902704440179 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993804)
  • known disease mutation: rs17933 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706735A>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000375323
Genbank transcript ID N/A
UniProt peptide P02647
alteration type single base exchange
alteration region CDS
DNA changes c.593T>C
cDNA.820T>C
g.1932T>C
AA changes L198S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs121912729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17933 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7950.124
1.2670.111
(flanking)0.1240.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1933wt: 0.45 / mu: 0.81wt: CGCTTGGCCGCGCGC
mu: CGCTCGGCCGCGCGC		 CTTG|gccg
distance from splice site 269
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198LAPYSDELRQRLAARLEALKENGG
mutated  not conserved    198LAPYSDELRQRSAARLEALKENG
Ptroglodytes  all identical  ENSPTRG00000004316  198LAPYSDELRQRLAARLEALKENG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  197LAPHSEQMRESLAQRLAELKSN-
Ggallus  all identical  ENSGALG00000007114  183RQKLSQKLEEIREKG
Trubripes  all identical  ENSTRUG00000007686  194LMPIVEKVHTKLAEYVEQIKAVV
Drerio  all conserved  ENSDARG00000086583  212LEPYVQEYKDQM--------EKG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  190LTPYSEEVRVKLVEKLEELKANA
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
166203HELIXlost
189210REPEAT7.lost
211232REPEAT8.might get lost (downstream of altered splice site)
212214TURNmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
220237HELIXmight get lost (downstream of altered splice site)
233243REPEAT9; half-length.might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
243266HELIXmight get lost (downstream of altered splice site)
244267REPEAT10.might get lost (downstream of altered splice site)
263263CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 1031 / 1031
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 228 / 228
chromosome 11
strand -1
last intron/exon boundary 428
theoretical NMD boundary in CDS 150
length of CDS 804
coding sequence (CDS) position 593
cDNA position
(for ins/del: last normal base / first normal base)		 820
gDNA position
(for ins/del: last normal base / first normal base)		 1932
chromosomal position
(for ins/del: last normal base / first normal base)		 116706735
original gDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered gDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
original cDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered cDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
wildtype AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
mutated AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRSAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.81 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.00175902704440179 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993804)
  • known disease mutation: rs17933 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706735A>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000236850
Genbank transcript ID NM_000039
UniProt peptide P02647
alteration type single base exchange
alteration region CDS
DNA changes c.593T>C
cDNA.959T>C
g.1932T>C
AA changes L198S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs121912729
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17933 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993804)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7950.124
1.2670.111
(flanking)0.1240.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1933wt: 0.45 / mu: 0.81wt: CGCTTGGCCGCGCGC
mu: CGCTCGGCCGCGCGC		 CTTG|gccg
distance from splice site 269
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198LAPYSDELRQRLAARLEALKENGG
mutated  not conserved    198LAPYSDELRQRSAARLEALKENG
Ptroglodytes  all identical  ENSPTRG00000004316  198LAPYSDELRQRLAARLEALKENG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  197LAPHSEQMRESLAQRLAELKSN-
Ggallus  all identical  ENSGALG00000007114  183RQKLSQKLEEIREKG
Trubripes  all identical  ENSTRUG00000007686  194LMPIVEKVHTKLAEYVEQIKAVV
Drerio  all conserved  ENSDARG00000086583  212LEPYVQEYKDQM--------EKG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  190LTPYSEEVRVKLVEKLEELKANA
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
166203HELIXlost
189210REPEAT7.lost
211232REPEAT8.might get lost (downstream of altered splice site)
212214TURNmight get lost (downstream of altered splice site)
215217STRANDmight get lost (downstream of altered splice site)
220237HELIXmight get lost (downstream of altered splice site)
233243REPEAT9; half-length.might get lost (downstream of altered splice site)
238240STRANDmight get lost (downstream of altered splice site)
243266HELIXmight get lost (downstream of altered splice site)
244267REPEAT10.might get lost (downstream of altered splice site)
263263CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 1170 / 1170
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 367 / 367
chromosome 11
strand -1
last intron/exon boundary 567
theoretical NMD boundary in CDS 150
length of CDS 804
coding sequence (CDS) position 593
cDNA position
(for ins/del: last normal base / first normal base)		 959
gDNA position
(for ins/del: last normal base / first normal base)		 1932
chromosomal position
(for ins/del: last normal base / first normal base)		 116706735
original gDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered gDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
original cDNA sequence snippet CGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTC
altered cDNA sequence snippet CGACGAGCTGCGCCAGCGCTCGGCCGCGCGCCTTGAGGCTC
wildtype AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
mutated AA sequence MKAAVLTLAV LFLTGSQARH FWQQDEPPQS PWDRVKDLAT VYVDVLKDSG RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRSAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.87 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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