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 0.44 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