Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999910620187494 (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) chr6:29911207G>AN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000376806
Genbank transcript ID N/A
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.506G>A
cDNA.815G>A
g.2171G>A
AA changes R169H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 169
frameshift no
known variant Reference ID: rs1059520
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC38292510928938
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4230.626
-0.0860.6
(flanking)0.1120.643
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2176wt: 0.34 / mu: 0.58wt: GCAAGTGGGAGGCGG
mu: ACAAGTGGGAGGCGG		 AAGT|ggga
Donor increased2175wt: 0.30 / mu: 0.52wt: CGCAAGTGGGAGGCG
mu: CACAAGTGGGAGGCG		 CAAG|tggg
distance from splice site 114
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      169TAADMAAQITKRKWEAAHEAEQLR
mutated  not conserved    169TAADMAAQITKHKWEAAHEAEQL
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  169TAADMAAQNTQRKWEAAGVAEQW
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
25308TOPO_DOMExtracellular (Potential).lost
115206REGIONAlpha-2.lost
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209295DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333365TOPO_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 1116 / 1116
position (AA) of stopcodon in wt / mu AA sequence 372 / 372
position of stopcodon in wt / mu cDNA 1425 / 1425
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 310 / 310
chromosome 6
strand 1
last intron/exon boundary 1421
theoretical NMD boundary in CDS 1061
length of CDS 1116
coding sequence (CDS) position 506
cDNA position
(for ins/del: last normal base / first normal base)		 815
gDNA position
(for ins/del: last normal base / first normal base)		 2171
chromosomal position
(for ins/del: last normal base / first normal base)		 29911207
original gDNA sequence snippet GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG
altered gDNA sequence snippet GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG
original cDNA sequence snippet GGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATG
altered cDNA sequence snippet GGCGGCTCAGATCACCAAGCACAAGTGGGAGGCGGCCCATG
wildtype AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSGGE GVKDRKGGSY TQAASSDSAQ
GSDVSLTACK V*
mutated AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKHK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSGGE GVKDRKGGSY TQAASSDSAQ
GSDVSLTACK V*
speed 1.08 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