Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 5.96239858512939e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM870005)
  • known disease mutation: rs17902 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116703580A>GN/A show variant in all transcripts   IGV
HGNC symbol APOC3
Ensembl transcript ID ENST00000375345
Genbank transcript ID N/A
UniProt peptide P02656
alteration type single base exchange
alteration region CDS
DNA changes c.334A>G
cDNA.396A>G
g.3159A>G
AA changes T112A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 112
frameshift no
known variant Reference ID: rs121918381
databasehomozygous (G/G)heterozygousallele carriers
1000G011
ExAC044

known disease mutation: rs17902 (pathogenic for Apolipoprotein c-iii, nonglycosylated) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)

known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)
known disease mutation at this position, please check HGMD for details (HGMD ID CM870005)
regulatory features 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
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.8020
-0.0860
(flanking)0.0780
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained31530.85mu: AGGTCAGACCAGCTT GTCA|gacc
distance from splice site 101
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      112EFWDLDPEVRPTSAVAA*
mutated  not conserved    112EFWDLDPEVRPASAVAA
Ptroglodytes  all identical  ENSPTRG00000004315  112EFWDSDPEVRPTSAEAA
Mmulatta  all identical  ENSMMUG00000016126  94GFWDLNPEAKPTLAEAA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000032081  132GFWDSNPEDQPTPAI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 354 / 354
position (AA) of stopcodon in wt / mu AA sequence 118 / 118
position of stopcodon in wt / mu cDNA 416 / 416
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 63 / 63
chromosome 11
strand 1
last intron/exon boundary 296
theoretical NMD boundary in CDS 183
length of CDS 354
coding sequence (CDS) position 334
cDNA position
(for ins/del: last normal base / first normal base)		 396
gDNA position
(for ins/del: last normal base / first normal base)		 3159
chromosomal position
(for ins/del: last normal base / first normal base)		 116703580
original gDNA sequence snippet TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA
altered gDNA sequence snippet TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA
original cDNA sequence snippet TGGACCCTGAGGTCAGACCAACTTCAGCCGTGGCTGCCTGA
altered cDNA sequence snippet TGGACCCTGAGGTCAGACCAGCTTCAGCCGTGGCTGCCTGA
wildtype AA sequence MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVKDKFS EFWDLDPEVR PTSAVAA*
mutated AA sequence MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVKDKFS EFWDLDPEVR PASAVAA*
speed 0.97 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