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 4.540021 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APOA1disease_causing_automatic7.16040703753053e-07simple_aaeaffected0L62Rsingle base exchangers121912724show file
APOA1disease_causing_automatic1.30762063430333e-05simple_aaeaffected0L84Rsingle base exchangers121912724show file
APOA1disease_causing_automatic1.30762063430333e-05simple_aaeaffected0L84Rsingle base exchangers121912724show file
APOA1disease_causing_automatic1.30762063430333e-05simple_aaeaffected0L84Rsingle base exchangers121912724show file
APOA1disease_causing_automatic1.30762063430333e-05simple_aaeaffected0L84Rsingle base exchangers121912724show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 7.16040703753053e-07 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920057)
  • known disease mutation: rs17923 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707077A>CN/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.185T>G
cDNA.317T>G
g.1590T>G
AA changes L62R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 62
frameshift no
known variant Reference ID: rs121912724
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17923 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540
1.7550.003
(flanking)-0.2330
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 increased1583wt: 0.5638 / mu: 0.5813 (marginal change - not scored)wt: ACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTC
mu: ACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCTC		 ttca|GCAA
Acc increased1582wt: 0.30 / mu: 0.53wt: GACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCT
mu: GACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCT		 cttc|AGCA
Donor marginally increased1587wt: 0.9778 / mu: 0.9924 (marginal change - not scored)wt: CAGCAAGCTGCGCGA
mu: CAGCAAGCGGCGCGA		 GCAA|gctg
Donor increased1583wt: 0.78 / mu: 0.87wt: CCTTCAGCAAGCTGC
mu: CCTTCAGCAAGCGGC		 TTCA|gcaa
Donor marginally increased1582wt: 0.8259 / mu: 0.8577 (marginal change - not scored)wt: ACCTTCAGCAAGCTG
mu: ACCTTCAGCAAGCGG		 CTTC|agca
Donor gained15890.70mu: GCAAGCGGCGCGAAC AAGC|ggcg
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      62NWDSVTSTFSKLREQLGPVTQEFW
mutated  not conserved    62KRREQLGPVTQEF
Ptroglodytes  all identical  ENSPTRG00000004316  86NWDSVTSTFSKLREQLGPVTQEF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  85NWDTLGSTVSQLQERLGPLTRDF
Ggallus  all identical  ENSGALG00000007114  69NLDTLSAAAAKLREDMAPYYKEV
Trubripes  not conserved  ENSTRUG00000007686  98DSVVSTISDATSELRTSIQTD
Drerio  all conserved  ENSDARG00000086583  98VMDATNPIREKLNKDMEDL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  85KLDTFGTNAMNLRKQINPYVENI
protein features
start (aa)end (aa)featuredetails 
6165HELIXlost
6889REPEAT1.might get lost (downstream of altered splice site)
68267REGION10 X approximate tandem repeats.might get lost (downstream of altered splice site)
6973STRANDmight get lost (downstream of altered splice site)
8088HELIXmight get lost (downstream of altered splice site)
90111REPEAT2.might get lost (downstream of altered splice site)
93158HELIXmight get lost (downstream of altered splice site)
110110MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
112122REPEAT3; half-length.might get lost (downstream of altered splice site)
123144REPEAT4.might get lost (downstream of altered splice site)
136136MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
145166REPEAT5.might get lost (downstream of altered splice site)
159164TURNmight get lost (downstream of altered splice site)
166203HELIXmight get lost (downstream of altered splice site)
167188REPEAT6.might get lost (downstream of altered splice site)
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 185
cDNA position
(for ins/del: last normal base / first normal base)		 317
gDNA position
(for ins/del: last normal base / first normal base)		 1590
chromosomal position
(for ins/del: last normal base / first normal base)		 116707077
original gDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered gDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
original cDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered cDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
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
KRREQLGPVT QEFWDNLEKE TEGLRQEMSK DLEEVKAKVQ PYLDDFQKKW QEEMELYRQK
VEPLRAELQE GARQKLHELQ EKLSPLGEEM RDRARAHVDA LRTHLAPYSD ELRQRLAARL
EALKENGGAR LAEYHAKATE HLSTLSEKAK PALEDLRQGL LPVLESFKVS FLSALEEYTK
KLNTQ*
speed 0.62 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: 1.30762063430333e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920057)
  • known disease mutation: rs17923 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707077A>CN/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.251T>G
cDNA.330T>G
g.1590T>G
AA changes L84R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 84
frameshift no
known variant Reference ID: rs121912724
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17923 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540
1.7550.003
(flanking)-0.2330
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 increased1583wt: 0.5638 / mu: 0.5813 (marginal change - not scored)wt: ACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTC
mu: ACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCTC		 ttca|GCAA
Acc increased1582wt: 0.30 / mu: 0.53wt: GACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCT
mu: GACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCT		 cttc|AGCA
Donor marginally increased1587wt: 0.9778 / mu: 0.9924 (marginal change - not scored)wt: CAGCAAGCTGCGCGA
mu: CAGCAAGCGGCGCGA		 GCAA|gctg
Donor increased1583wt: 0.78 / mu: 0.87wt: CCTTCAGCAAGCTGC
mu: CCTTCAGCAAGCGGC		 TTCA|gcaa
Donor marginally increased1582wt: 0.8259 / mu: 0.8577 (marginal change - not scored)wt: ACCTTCAGCAAGCTG
mu: ACCTTCAGCAAGCGG		 CTTC|agca
Donor gained15890.70mu: GCAAGCGGCGCGAAC AAGC|ggcg
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      84NWDSVTSTFSKLREQLGPVTQEFW
mutated  not conserved    84NWDSVTSTFSKRREQLGPVTQEF
Ptroglodytes  all identical  ENSPTRG00000004316  84NWDSVTSTFSKLREQLGPVTQEF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  83NWDTLGSTVSQLQERLGPLTRDF
Ggallus  all identical  ENSGALG00000007114  69DTLSAAAAKLREDMAPYYKEV
Trubripes  all identical  ENSTRUG00000007686  81RVDDIHSQIKTLQGSVSPITDSV
Drerio  not conserved  ENSDARG00000086583  81SIDNLHSHFQNFFQVITPLGSQV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  83KLDTFGTNAMNLRKQINPYVENI
protein features
start (aa)end (aa)featuredetails 
6889REPEAT1.lost
68267REGION10 X approximate tandem repeats.lost
8088HELIXlost
90111REPEAT2.might get lost (downstream of altered splice site)
93158HELIXmight get lost (downstream of altered splice site)
110110MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
112122REPEAT3; half-length.might get lost (downstream of altered splice site)
123144REPEAT4.might get lost (downstream of altered splice site)
136136MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
145166REPEAT5.might get lost (downstream of altered splice site)
159164TURNmight get lost (downstream of altered splice site)
166203HELIXmight get lost (downstream of altered splice site)
167188REPEAT6.might get lost (downstream of altered splice site)
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 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 251
cDNA position
(for ins/del: last normal base / first normal base)		 330
gDNA position
(for ins/del: last normal base / first normal base)		 1590
chromosomal position
(for ins/del: last normal base / first normal base)		 116707077
original gDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered gDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
original cDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered cDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
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 FSKRREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.77 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: 1.30762063430333e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920057)
  • known disease mutation: rs17923 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707077A>CN/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.251T>G
cDNA.322T>G
g.1590T>G
AA changes L84R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 84
frameshift no
known variant Reference ID: rs121912724
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17923 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540
1.7550.003
(flanking)-0.2330
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 increased1583wt: 0.5638 / mu: 0.5813 (marginal change - not scored)wt: ACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTC
mu: ACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCTC		 ttca|GCAA
Acc increased1582wt: 0.30 / mu: 0.53wt: GACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCT
mu: GACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCT		 cttc|AGCA
Donor marginally increased1587wt: 0.9778 / mu: 0.9924 (marginal change - not scored)wt: CAGCAAGCTGCGCGA
mu: CAGCAAGCGGCGCGA		 GCAA|gctg
Donor increased1583wt: 0.78 / mu: 0.87wt: CCTTCAGCAAGCTGC
mu: CCTTCAGCAAGCGGC		 TTCA|gcaa
Donor marginally increased1582wt: 0.8259 / mu: 0.8577 (marginal change - not scored)wt: ACCTTCAGCAAGCTG
mu: ACCTTCAGCAAGCGG		 CTTC|agca
Donor gained15890.70mu: GCAAGCGGCGCGAAC AAGC|ggcg
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      84NWDSVTSTFSKLREQLGPVTQEFW
mutated  not conserved    84NWDSVTSTFSKRREQLGPVTQEF
Ptroglodytes  all identical  ENSPTRG00000004316  84NWDSVTSTFSKLREQLGPVTQEF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  83NWDTLGSTVSQLQERLGPLTRDF
Ggallus  all identical  ENSGALG00000007114  69DTLSAAAAKLREDMAPYYKEV
Trubripes  all identical  ENSTRUG00000007686  81RVDDIHSQIKTLQGSVSPITDSV
Drerio  not conserved  ENSDARG00000086583  81SIDNLHSHFQNFFQVITPLGSQV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  83KLDTFGTNAMNLRKQINPYVENI
protein features
start (aa)end (aa)featuredetails 
6889REPEAT1.lost
68267REGION10 X approximate tandem repeats.lost
8088HELIXlost
90111REPEAT2.might get lost (downstream of altered splice site)
93158HELIXmight get lost (downstream of altered splice site)
110110MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
112122REPEAT3; half-length.might get lost (downstream of altered splice site)
123144REPEAT4.might get lost (downstream of altered splice site)
136136MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
145166REPEAT5.might get lost (downstream of altered splice site)
159164TURNmight get lost (downstream of altered splice site)
166203HELIXmight get lost (downstream of altered splice site)
167188REPEAT6.might get lost (downstream of altered splice site)
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 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 251
cDNA position
(for ins/del: last normal base / first normal base)		 322
gDNA position
(for ins/del: last normal base / first normal base)		 1590
chromosomal position
(for ins/del: last normal base / first normal base)		 116707077
original gDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered gDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
original cDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered cDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
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 FSKRREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
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: 1.30762063430333e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920057)
  • known disease mutation: rs17923 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707077A>CN/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.251T>G
cDNA.478T>G
g.1590T>G
AA changes L84R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 84
frameshift no
known variant Reference ID: rs121912724
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17923 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540
1.7550.003
(flanking)-0.2330
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 increased1583wt: 0.5638 / mu: 0.5813 (marginal change - not scored)wt: ACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTC
mu: ACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCTC		 ttca|GCAA
Acc increased1582wt: 0.30 / mu: 0.53wt: GACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCT
mu: GACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCT		 cttc|AGCA
Donor marginally increased1587wt: 0.9778 / mu: 0.9924 (marginal change - not scored)wt: CAGCAAGCTGCGCGA
mu: CAGCAAGCGGCGCGA		 GCAA|gctg
Donor increased1583wt: 0.78 / mu: 0.87wt: CCTTCAGCAAGCTGC
mu: CCTTCAGCAAGCGGC		 TTCA|gcaa
Donor marginally increased1582wt: 0.8259 / mu: 0.8577 (marginal change - not scored)wt: ACCTTCAGCAAGCTG
mu: ACCTTCAGCAAGCGG		 CTTC|agca
Donor gained15890.70mu: GCAAGCGGCGCGAAC AAGC|ggcg
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      84NWDSVTSTFSKLREQLGPVTQEFW
mutated  not conserved    84NWDSVTSTFSKRREQLGPVTQEF
Ptroglodytes  all identical  ENSPTRG00000004316  84NWDSVTSTFSKLREQLGPVTQEF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  83NWDTLGSTVSQLQERLGPLTRDF
Ggallus  all identical  ENSGALG00000007114  69DTLSAAAAKLREDMAPYYKEV
Trubripes  all identical  ENSTRUG00000007686  81RVDDIHSQIKTLQGSVSPITDSV
Drerio  not conserved  ENSDARG00000086583  81SIDNLHSHFQNFFQVITPLGSQV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  83KLDTFGTNAMNLRKQINPYVENI
protein features
start (aa)end (aa)featuredetails 
6889REPEAT1.lost
68267REGION10 X approximate tandem repeats.lost
8088HELIXlost
90111REPEAT2.might get lost (downstream of altered splice site)
93158HELIXmight get lost (downstream of altered splice site)
110110MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
112122REPEAT3; half-length.might get lost (downstream of altered splice site)
123144REPEAT4.might get lost (downstream of altered splice site)
136136MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
145166REPEAT5.might get lost (downstream of altered splice site)
159164TURNmight get lost (downstream of altered splice site)
166203HELIXmight get lost (downstream of altered splice site)
167188REPEAT6.might get lost (downstream of altered splice site)
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 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 251
cDNA position
(for ins/del: last normal base / first normal base)		 478
gDNA position
(for ins/del: last normal base / first normal base)		 1590
chromosomal position
(for ins/del: last normal base / first normal base)		 116707077
original gDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered gDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
original cDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered cDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
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 FSKRREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
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: 1.30762063430333e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920057)
  • known disease mutation: rs17923 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707077A>CN/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.251T>G
cDNA.617T>G
g.1590T>G
AA changes L84R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 84
frameshift no
known variant Reference ID: rs121912724
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17923 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920057)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540
1.7550.003
(flanking)-0.2330
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 increased1583wt: 0.5638 / mu: 0.5813 (marginal change - not scored)wt: ACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCTC
mu: ACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCTC		 ttca|GCAA
Acc increased1582wt: 0.30 / mu: 0.53wt: GACAGCGTGACCTCCACCTTCAGCAAGCTGCGCGAACAGCT
mu: GACAGCGTGACCTCCACCTTCAGCAAGCGGCGCGAACAGCT		 cttc|AGCA
Donor marginally increased1587wt: 0.9778 / mu: 0.9924 (marginal change - not scored)wt: CAGCAAGCTGCGCGA
mu: CAGCAAGCGGCGCGA		 GCAA|gctg
Donor increased1583wt: 0.78 / mu: 0.87wt: CCTTCAGCAAGCTGC
mu: CCTTCAGCAAGCGGC		 TTCA|gcaa
Donor marginally increased1582wt: 0.8259 / mu: 0.8577 (marginal change - not scored)wt: ACCTTCAGCAAGCTG
mu: ACCTTCAGCAAGCGG		 CTTC|agca
Donor gained15890.70mu: GCAAGCGGCGCGAAC AAGC|ggcg
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      84NWDSVTSTFSKLREQLGPVTQEFW
mutated  not conserved    84NWDSVTSTFSKRREQLGPVTQEF
Ptroglodytes  all identical  ENSPTRG00000004316  84NWDSVTSTFSKLREQLGPVTQEF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  83NWDTLGSTVSQLQERLGPLTRDF
Ggallus  all identical  ENSGALG00000007114  69DTLSAAAAKLREDMAPYYKEV
Trubripes  all identical  ENSTRUG00000007686  81RVDDIHSQIKTLQGSVSPITDSV
Drerio  not conserved  ENSDARG00000086583  81SIDNLHSHFQNFFQVITPLGSQV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  83KLDTFGTNAMNLRKQINPYVENI
protein features
start (aa)end (aa)featuredetails 
6889REPEAT1.lost
68267REGION10 X approximate tandem repeats.lost
8088HELIXlost
90111REPEAT2.might get lost (downstream of altered splice site)
93158HELIXmight get lost (downstream of altered splice site)
110110MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
112122REPEAT3; half-length.might get lost (downstream of altered splice site)
123144REPEAT4.might get lost (downstream of altered splice site)
136136MOD_RESMethionine sulfoxide.might get lost (downstream of altered splice site)
145166REPEAT5.might get lost (downstream of altered splice site)
159164TURNmight get lost (downstream of altered splice site)
166203HELIXmight get lost (downstream of altered splice site)
167188REPEAT6.might get lost (downstream of altered splice site)
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 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 251
cDNA position
(for ins/del: last normal base / first normal base)		 617
gDNA position
(for ins/del: last normal base / first normal base)		 1590
chromosomal position
(for ins/del: last normal base / first normal base)		 116707077
original gDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered gDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
original cDNA sequence snippet GACCTCCACCTTCAGCAAGCTGCGCGAACAGCTCGGCCCTG
altered cDNA sequence snippet GACCTCCACCTTCAGCAAGCGGCGCGAACAGCTCGGCCCTG
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 FSKRREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.76 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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