Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997956092 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990165)
  • known disease mutation: rs17931 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706987A>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.341T>C
cDNA.420T>C
g.1680T>C
AA changes L114P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 114
frameshift no
known variant Reference ID: rs28931575
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17931 (pathogenic for Amyloidosis, cardiac and cutaneous) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990165)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990165)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990165)
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
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
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)2.0660.983
3.760.995
(flanking)1.3770.984
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 increased1681wt: 0.9532 / mu: 0.9830 (marginal change - not scored)wt: GATCTGGAGGAGGTG
mu: GATCCGGAGGAGGTG		 TCTG|gagg
distance from splice site 141
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      114TEGLRQEMSKDLEEVKAKVQPYLD
mutated  not conserved    114TEGLRQEMSKDPEEVKAK
Ptroglodytes  all identical  ENSPTRG00000004316  114TEGLRQEMSKDLEEVKAK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  113TDWVRQEMNKDLEEVKQK
Ggallus  all identical  ENSGALG00000007114  99TEALRAELTKDLEEVKEKIRPFL
Trubripes  not conserved  ENSTRUG00000007686  111TSELRTSIQTDFKTLQDE
Drerio  not conserved  ENSDARG00000086583  117REELRAVLEKHFNEYRDELKPFM
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003763  113LE-------KELPVIKEK
protein features
start (aa)end (aa)featuredetails 
68267REGION10 X approximate tandem repeats.lost
93158HELIXlost
112122REPEAT3; half-length.lost
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 341
cDNA position
(for ins/del: last normal base / first normal base)		 420
gDNA position
(for ins/del: last normal base / first normal base)		 1680
chromosomal position
(for ins/del: last normal base / first normal base)		 116706987
original gDNA sequence snippet GCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGG
altered gDNA sequence snippet GCAGGAGATGAGCAAGGATCCGGAGGAGGTGAAGGCCAAGG
original cDNA sequence snippet GCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGG
altered cDNA sequence snippet GCAGGAGATGAGCAAGGATCCGGAGGAGGTGAAGGCCAAGG
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 SKDPEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.28 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