Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998818 (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) chr6:29910358C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000376802
Genbank transcript ID N/A
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.28C>G
cDNA.33C>G
g.1322C>G
AA changes L10V Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 10
frameshift no
known variant Reference ID: rs1143146
databasehomozygous (G/G)heterozygousallele carriers
1000G61113091920
ExAC13793518118974
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
FAIRE, Open Chromatin, Formaldehyde-Assisted Isolation of Regulatory Elements
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5230.006
-0.0690.006
(flanking)2.0040.012
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1326wt: 0.23 / mu: 0.33wt: CCTCCTGCTACTCTC
mu: CGTCCTGCTACTCTC		 TCCT|gcta
Donor gained13160.67mu: CCCGAACCCTCGTCC CGAA|ccct
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      10 MAVMAPRTLLLLLSGALALTQT
mutated  all conserved    10 MAVMAPRTLVLLLSGALALTQT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  10 MAVMAPRTLLLVLSGALALTQT
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 
124SIGNALlost
25114REGIONAlpha-1.might get lost (downstream of altered splice site)
25308TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...) (By similarity).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
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 900 / 900
position (AA) of stopcodon in wt / mu AA sequence 300 / 300
position of stopcodon in wt / mu cDNA 905 / 905
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 6 / 6
chromosome 6
strand 1
last intron/exon boundary 901
theoretical NMD boundary in CDS 845
length of CDS 900
coding sequence (CDS) position 28
cDNA position
(for ins/del: last normal base / first normal base)		 33
gDNA position
(for ins/del: last normal base / first normal base)		 1322
chromosomal position
(for ins/del: last normal base / first normal base)		 29910358
original gDNA sequence snippet TCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCC
altered gDNA sequence snippet TCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCC
original cDNA sequence snippet TCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCC
altered cDNA sequence snippet TCATGGCGCCCCGAACCCTCGTCCTGCTACTCTCGGGGGCC
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 PKPLTLRWV*
mutated AA sequence MAVMAPRTLV 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 PKPLTLRWV*
speed 1.02 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