Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 9.35807618236075e-09 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM149600)
  • known disease mutation at this position (HGMD CM950074)
  • known disease mutation: rs17928 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116707108A>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.220T>C
cDNA.586T>C
g.1559T>C
AA changes W74R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 74
frameshift no
known variant Reference ID: rs121912726
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17928 (pathogenic for Familial visceral amyloidosis, Ostertag type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950074)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950074)
known disease mutation at this position, please check HGMD for details (HGMD ID CM149600)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950074)
known disease mutation at this position, please check HGMD for details (HGMD ID CM149600)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950074)
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)-0.2560.075
0.5170.108
(flanking)1.0580.15
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 increased1560wt: 0.5548 / mu: 0.5967 (marginal change - not scored)wt: CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCT
mu: CCTAAAGCTCCTTGACAACCGGGACAGCGTGACCTCCACCT		 actg|GGAC
Donor increased1560wt: 0.42 / mu: 0.74wt: CAACTGGGACAGCGT
mu: CAACCGGGACAGCGT		 ACTG|ggac
Donor gained15590.32mu: ACAACCGGGACAGCG AACC|ggga
distance from splice site 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      74GKQLNLKLLDNWDSVTSTFSKLRE
mutated  not conserved    74GKQLNLKLLDNRDSVTSTFSKLR
Ptroglodytes  all identical  ENSPTRG00000004316  74GKQLNLKLLDNWDSVTSTFSKLR
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032083  73GQQLNLNLLENWDTLGSTVSQLQ
Ggallus  not conserved  ENSGALG00000007114  60GKQLDLKLADNLDTLSAAAAKLR
Trubripes  not conserved  ENSTRUG00000007686  71-KELKDRLAQRVDDIHSQIKTLQ
Drerio  not conserved  ENSDARG00000086583  71-KDYKVFLGQSIDNLHSHFQNFF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000003763  73GKQLDLKITEKLDTFGTNAMNLR
protein features
start (aa)end (aa)featuredetails 
6889REPEAT1.lost
68267REGION10 X approximate tandem repeats.lost
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 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 220
cDNA position
(for ins/del: last normal base / first normal base)		 586
gDNA position
(for ins/del: last normal base / first normal base)		 1559
chromosomal position
(for ins/del: last normal base / first normal base)		 116707108
original gDNA sequence snippet GCCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACC
altered gDNA sequence snippet GCCTAAAGCTCCTTGACAACCGGGACAGCGTGACCTCCACC
original cDNA sequence snippet ACCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACC
altered cDNA sequence snippet ACCTAAAGCTCCTTGACAACCGGGACAGCGTGACCTCCACC
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 LDNRDSVTST FSKLREQLGP VTQEFWDNLE KETEGLRQEM SKDLEEVKAK
VQPYLDDFQK KWQEEMELYR QKVEPLRAEL QEGARQKLHE LQEKLSPLGE EMRDRARAHV
DALRTHLAPY SDELRQRLAA RLEALKENGG ARLAEYHAKA TEHLSTLSEK AKPALEDLRQ
GLLPVLESFK VSFLSALEEY TKKLNTQ*
speed 1.20 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