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 8.428068 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APOA1disease_causing_automatic0.998386456556493simple_aae0G50Rsingle base exchangers28931574show file
APOA1disease_causing_automatic0.998386456556493simple_aae0G50Rsingle base exchangers28931574show file
APOA1disease_causing_automatic0.998386456556493simple_aae0G50Rsingle base exchangers28931574show file
APOA1disease_causing_automatic0.998386456556493simple_aae0G50Rsingle base exchangers28931574show file
APOA1disease_causing_automatic1without_aae0single base exchangers28931574show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998386456556493 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900016)
  • known disease mutation: rs17917 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707769C>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.148G>C
cDNA.227G>C
g.898G>C
AA changes G50R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
50
frameshift no
known variant Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
regulatory features 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
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3761
2.4810.978
(flanking)-0.4860.024
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased898wt: 0.9817 / mu: 0.9938 (marginal change - not scored)wt: ACAGCGGCAGAGACT
mu: ACAGCCGCAGAGACT
 AGCG|gcag
Donor marginally increased901wt: 0.7917 / mu: 0.8707 (marginal change - not scored)wt: GCGGCAGAGACTATG
mu: GCCGCAGAGACTATG
 GGCA|gaga
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50ATVYVDVLKDSGRDYVSQFEGSAL
mutated  not conserved    50ATVYVDVLKDSRRDYVSQFEGS
Ptroglodytes  all identical  ENSPTRG00000004316  50ATVYVDVLKDSGRDYVSQFEGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  50ANVYVDAVKDSGRDYVSQFESS
Ggallus  all identical  ENSGALG00000007114  36VDVYLETVKASGKDAIAQFESSA
Trubripes  not conserved  ENSTRUG00000007686  50LSMYLDRAKERAHSALATLDDA
Drerio  not conserved  ENSDARG00000086583  51LQVYADHLKQAAHKSLTHLDDT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  50LESYVHKVRDLGREAVSQLETS
protein features
start (aa)end (aa)featuredetails 
4559HELIXlost
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 148
cDNA position
(for ins/del: last normal base / first normal base)
227
gDNA position
(for ins/del: last normal base / first normal base)
898
chromosomal position
(for ins/del: last normal base / first normal base)
116707769
original gDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered gDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
original cDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered cDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
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 VYVDVLKDSR RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.38 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: 0.998386456556493 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900016)
  • known disease mutation: rs17917 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707769C>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.148G>C
cDNA.219G>C
g.898G>C
AA changes G50R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
50
frameshift no
known variant Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
regulatory features 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
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3761
2.4810.978
(flanking)-0.4860.024
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased898wt: 0.9817 / mu: 0.9938 (marginal change - not scored)wt: ACAGCGGCAGAGACT
mu: ACAGCCGCAGAGACT
 AGCG|gcag
Donor marginally increased901wt: 0.7917 / mu: 0.8707 (marginal change - not scored)wt: GCGGCAGAGACTATG
mu: GCCGCAGAGACTATG
 GGCA|gaga
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50ATVYVDVLKDSGRDYVSQFEGSAL
mutated  not conserved    50ATVYVDVLKDSRRDYVSQFEGS
Ptroglodytes  all identical  ENSPTRG00000004316  50ATVYVDVLKDSGRDYVSQFEGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  50ANVYVDAVKDSGRDYVSQFESS
Ggallus  all identical  ENSGALG00000007114  36VDVYLETVKASGKDAIAQFESSA
Trubripes  not conserved  ENSTRUG00000007686  50LSMYLDRAKERAHSALATLDDA
Drerio  not conserved  ENSDARG00000086583  51LQVYADHLKQAAHKSLTHLDDT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  50LESYVHKVRDLGREAVSQLETS
protein features
start (aa)end (aa)featuredetails 
4559HELIXlost
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 148
cDNA position
(for ins/del: last normal base / first normal base)
219
gDNA position
(for ins/del: last normal base / first normal base)
898
chromosomal position
(for ins/del: last normal base / first normal base)
116707769
original gDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered gDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
original cDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered cDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
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 VYVDVLKDSR RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.46 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998386456556493 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900016)
  • known disease mutation: rs17917 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707769C>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.148G>C
cDNA.375G>C
g.898G>C
AA changes G50R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
50
frameshift no
known variant Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
regulatory features 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
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3761
2.4810.978
(flanking)-0.4860.024
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased898wt: 0.9817 / mu: 0.9938 (marginal change - not scored)wt: ACAGCGGCAGAGACT
mu: ACAGCCGCAGAGACT
 AGCG|gcag
Donor marginally increased901wt: 0.7917 / mu: 0.8707 (marginal change - not scored)wt: GCGGCAGAGACTATG
mu: GCCGCAGAGACTATG
 GGCA|gaga
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50ATVYVDVLKDSGRDYVSQFEGSAL
mutated  not conserved    50ATVYVDVLKDSRRDYVSQFEGS
Ptroglodytes  all identical  ENSPTRG00000004316  50ATVYVDVLKDSGRDYVSQFEGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  50ANVYVDAVKDSGRDYVSQFESS
Ggallus  all identical  ENSGALG00000007114  36VDVYLETVKASGKDAIAQFESSA
Trubripes  not conserved  ENSTRUG00000007686  50LSMYLDRAKERAHSALATLDDA
Drerio  not conserved  ENSDARG00000086583  51LQVYADHLKQAAHKSLTHLDDT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  50LESYVHKVRDLGREAVSQLETS
protein features
start (aa)end (aa)featuredetails 
4559HELIXlost
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 148
cDNA position
(for ins/del: last normal base / first normal base)
375
gDNA position
(for ins/del: last normal base / first normal base)
898
chromosomal position
(for ins/del: last normal base / first normal base)
116707769
original gDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered gDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
original cDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered cDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
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 VYVDVLKDSR RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.46 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998386456556493 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM900016)
  • known disease mutation: rs17917 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707769C>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.148G>C
cDNA.514G>C
g.898G>C
AA changes G50R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
50
frameshift no
known variant Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
regulatory features 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
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3761
2.4810.978
(flanking)-0.4860.024
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased898wt: 0.9817 / mu: 0.9938 (marginal change - not scored)wt: ACAGCGGCAGAGACT
mu: ACAGCCGCAGAGACT
 AGCG|gcag
Donor marginally increased901wt: 0.7917 / mu: 0.8707 (marginal change - not scored)wt: GCGGCAGAGACTATG
mu: GCCGCAGAGACTATG
 GGCA|gaga
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50ATVYVDVLKDSGRDYVSQFEGSAL
mutated  not conserved    50ATVYVDVLKDSRRDYVSQFEGS
Ptroglodytes  all identical  ENSPTRG00000004316  50ATVYVDVLKDSGRDYVSQFEGS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  50ANVYVDAVKDSGRDYVSQFESS
Ggallus  all identical  ENSGALG00000007114  36VDVYLETVKASGKDAIAQFESSA
Trubripes  not conserved  ENSTRUG00000007686  50LSMYLDRAKERAHSALATLDDA
Drerio  not conserved  ENSDARG00000086583  51LQVYADHLKQAAHKSLTHLDDT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  50LESYVHKVRDLGREAVSQLETS
protein features
start (aa)end (aa)featuredetails 
4559HELIXlost
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 148
cDNA position
(for ins/del: last normal base / first normal base)
514
gDNA position
(for ins/del: last normal base / first normal base)
898
chromosomal position
(for ins/del: last normal base / first normal base)
116707769
original gDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered gDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
original cDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered cDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
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 VYVDVLKDSR RDYVSQFEGS
ALGKQLNLKL LDNWDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.33 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM900016)
  • known disease mutation: rs17917 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707769C>GN/A show variant in all transcripts   IGV
HGNC symbol APOA1
Ensembl transcript ID ENST00000375329
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.898G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs28931574
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17917 (pathogenic for Familial amyloid polyneuropathy, Iowa type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900016)
regulatory features 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
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3761
2.4810.978
(flanking)-0.4860.024
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased898wt: 0.9817 / mu: 0.9938 (marginal change - not scored)wt: ACAGCGGCAGAGACT
mu: ACAGCCGCAGAGACT
 AGCG|gcag
Donor marginally increased901wt: 0.7917 / mu: 0.8707 (marginal change - not scored)wt: GCGGCAGAGACTATG
mu: GCCGCAGAGACTATG
 GGCA|gaga
distance from splice site 292
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
898
chromosomal position
(for ins/del: last normal base / first normal base)
116707769
original gDNA sequence snippet TGGATGTGCTCAAAGACAGCGGCAGAGACTATGTGTCCCAG
altered gDNA sequence snippet TGGATGTGCTCAAAGACAGCCGCAGAGACTATGTGTCCCAG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
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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