Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999978702 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:32629935C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB1
Ensembl transcript ID ENST00000399084
Genbank transcript ID N/A
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.470G>C
cDNA.649G>C
g.6226G>C
AA changes G157A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 157
frameshift no
known variant Reference ID: rs1063322
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC18865-496313902
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.170.003
-0.060.001
(flanking)-0.5190.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased6223wt: 0.61 / mu: 0.69wt: CTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGT
mu: CTCGGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGT		 atcc|AGGC
Donor increased6224wt: 0.75 / mu: 0.88wt: TATCCAGGCCAGATC
mu: TATCCAGCCCAGATC		 TCCA|ggcc
Donor gained62290.40mu: AGCCCAGATCAAAGT CCCA|gatc
distance from splice site 91
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      157LLVCSVTDFYPGQIKVRWFRNDQE
mutated  not conserved    157LLVCSVTDFYPAQIKVRWFRNDQ
Ptroglodytes  all identical  ENSPTRG00000018018  157LLVCSVTDFYPGQIKVRWFRNDQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000073421  152TLVCSVTDFYPAKIKVRWFRNGQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000079105  142VLLCSAYEFYPKKIKMSWLRDGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
129233DOMAINIg-like C1-type.lost
147157STRANDlost
160165STRANDmight get lost (downstream of altered splice site)
168170STRANDmight get lost (downstream of altered splice site)
172176STRANDmight get lost (downstream of altered splice site)
173173CONFLICTG -> A (in Ref. 24; X76553/X76554).might get lost (downstream of altered splice site)
183185STRANDmight get lost (downstream of altered splice site)
187193STRANDmight get lost (downstream of altered splice site)
203208STRANDmight get lost (downstream of altered splice site)
205205DISULFIDmight get lost (downstream of altered splice site)
214214CONFLICTN -> T (in Ref. 8; AAA59770).might get lost (downstream of altered splice site)
216220STRANDmight get lost (downstream of altered splice site)
221230REGIONConnecting peptide.might get lost (downstream of altered splice site)
231251TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
252261TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 965 / 965
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 180 / 180
chromosome 6
strand -1
last intron/exon boundary 952
theoretical NMD boundary in CDS 722
length of CDS 786
coding sequence (CDS) position 470
cDNA position
(for ins/del: last normal base / first normal base)		 649
gDNA position
(for ins/del: last normal base / first normal base)		 6226
chromosomal position
(for ins/del: last normal base / first normal base)		 32629935
original gDNA sequence snippet GGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGTGGT
altered gDNA sequence snippet GGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGTGGT
original cDNA sequence snippet GGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGTGGT
altered cDNA sequence snippet GGTGACAGATTTCTATCCAGCCCAGATCAAAGTCCGGTGGT
wildtype AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
mutated AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPEDFV FQFKGMCYFT NGTERVRLVT
RYIYNREEYA RFDSDVGVYR AVTPQGRPDA EYWNSQKEVL EGTRAELDTV CRHNYEVAFR
GILQRRVEPT VTISPSRTEA LNHHNLLVCS VTDFYPAQIK VRWFRNDQEE TAGVVSTPLI
RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP SLQSPITVEW RAQSESAQSK MLSGVGGFVL
GLIFLGLGLI IRQRSQKGLL H*
speed 0.47 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