Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999997730659 (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
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:32629755G>AN/A show variant in all transcripts   IGV
HGNC symbol HLA-DQB1
Ensembl transcript ID ENST00000399082
Genbank transcript ID N/A
UniProt peptide P01920
alteration type single base exchange
alteration region CDS
DNA changes c.380C>T
cDNA.425C>T
g.6406C>T
AA changes T127I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 127
frameshift no
known variant Reference ID: rs1130399
databasehomozygous (A/A)heterozygousallele carriers
1000G1898961085
ExAC35611885822419
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.240.002
0.1530.006
(flanking)0.2260.022
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 increased6407wt: 0.9821 / mu: 0.9867 (marginal change - not scored)wt: ATCACCGTGGAGTGG
mu: ATCATCGTGGAGTGG		 CACC|gtgg
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      127HVEHPSLQSPITVEWRLLH*
mutated  not conserved    127SLQSPIIVEWRLLH
Ptroglodytes  all identical  ENSPTRG00000018018  217HVEHPSLQNPITVEWR
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000073421  213HVEHPSLKSPITVEWR
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000079105  202LVEHASLTQPLTKDW
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
33230TOPO_DOMExtracellular (Potential).lost
127220REGIONBeta-2.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 405 / 405
position (AA) of stopcodon in wt / mu AA sequence 135 / 135
position of stopcodon in wt / mu cDNA 450 / 450
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 46 / 46
chromosome 6
strand -1
last intron/exon boundary 437
theoretical NMD boundary in CDS 341
length of CDS 405
coding sequence (CDS) position 380
cDNA position
(for ins/del: last normal base / first normal base)		 425
gDNA position
(for ins/del: last normal base / first normal base)		 6406
chromosomal position
(for ins/del: last normal base / first normal base)		 32629755
original gDNA sequence snippet CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGTAAGGGGA
altered gDNA sequence snippet CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGTAAGGGGA
original cDNA sequence snippet CAGCCTCCAGAGCCCCATCACCGTGGAGTGGCGGCTTCTGC
altered cDNA sequence snippet CAGCCTCCAGAGCCCCATCATCGTGGAGTGGCGGCTTCTGC
wildtype AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS
VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP
SLQSPITVEW RLLH*
mutated AA sequence MSWKKALRIP GDLRVATVTL MLAMLSSLLA EGRDSPVEPT VTISPSRTEA LNHHNLLVCS
VTDFYPGQIK VRWFRNDQEE TAGVVSTPLI RNGDWTFQIL VMLEMTPQRG DVYTCHVEHP
SLQSPIIVEW RLLH*
speed 0.94 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