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mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999828537      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990166)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116706738C>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.590G>C
cDNA.661G>C
g.1929G>C
AA changes R197P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 197
frameshift no
known variant Reference ID: rs121912728
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM990166)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990166)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990166)
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)0.0250.003
0.3540.002
(flanking)0.0370.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1940wt: 0.61 / mu: 0.76wt: TGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAG
mu: TGCGCCAGCCCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAG		 gcgc|GCCT
Donor increased1933wt: 0.45 / mu: 0.60wt: CGCTTGGCCGCGCGC
mu: CCCTTGGCCGCGCGC		 CTTG|gccg
distance from splice site 272
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      197HLAPYSDELRQRLAARLEALKENG
mutated  not conserved    197HLAPYSDELRQPLAARLEALKEN
Ptroglodytes  all identical  ENSPTRG00000004316  197HLAPYSDELRQRLAARLEALKEN
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000032083  196QLAPHSEQMRESLAQRLAELKSN
Ggallus  all conserved  ENSGALG00000007114  182RQKLSQKLEEIREK
Trubripes  all conserved  ENSTRUG00000007686  193ALMPIVEKVHTKLAEYVEQIKAV
Drerio  all conserved  ENSDARG00000086583  211MLEPYVQEYKDQM--------EK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000003763  189RLTPYSEEVRVKLVEKLEELKAN
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 590
cDNA position
(for ins/del: last normal base / first normal base)		 661
gDNA position
(for ins/del: last normal base / first normal base)		 1929
chromosomal position
(for ins/del: last normal base / first normal base)		 116706738
original gDNA sequence snippet CAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGG
altered gDNA sequence snippet CAGCGACGAGCTGCGCCAGCCCTTGGCCGCGCGCCTTGAGG
original cDNA sequence snippet CAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGG
altered cDNA sequence snippet CAGCGACGAGCTGCGCCAGCCCTTGGCCGCGCGCCTTGAGG
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 SDELRQPLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 0.48 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