Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999638 (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) chr6:31239430C>TN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000539307
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.400G>A
cDNA.400G>A
g.478G>A
AA changes A134T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 134
frameshift no
known variant Reference ID: rs41543814
databasehomozygous (T/T)heterozygousallele carriers
1000G56111921753
ExAC11836909520931
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
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
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-6.2910
-1.0340
(flanking)0.2260.001
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 increased470wt: 0.8588 / mu: 0.8611 (marginal change - not scored)wt: GCGCCAGGCACAGGC
mu: GCGCCAGGCACAGAC		 GCCA|ggca
Donor marginally increased481wt: 0.8632 / mu: 0.9403 (marginal change - not scored)wt: AGGCTGACCGAGTGA
mu: AGACTGACCGAGTGA		 GCTG|accg
Donor marginally increased471wt: 0.7342 / mu: 0.7576 (marginal change - not scored)wt: CGCCAGGCACAGGCT
mu: CGCCAGGCACAGACT		 CCAG|gcac
distance from splice site 55
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      134RETQKYKRQAQADRVSLRNLRGYY
mutated  not conserved    134RETQKYKRQAQTDRVSLRNLRGY
Ptroglodytes  all identical  ENSPTRG00000041261  97RETQKYKRQAQADRVSLRNLRGY
Mmulatta  not conserved  ENSMMUG00000029841  93LETRGAKTHTENFQVNLTLLR-H
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
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1212 / 1212
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 1 / 1
chromosome 6
strand -1
last intron/exon boundary 1208
theoretical NMD boundary in CDS 1157
length of CDS 1212
coding sequence (CDS) position 400
cDNA position
(for ins/del: last normal base / first normal base)		 400
gDNA position
(for ins/del: last normal base / first normal base)		 478
chromosomal position
(for ins/del: last normal base / first normal base)		 31239430
original gDNA sequence snippet AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG
altered gDNA sequence snippet AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG
original cDNA sequence snippet AGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGG
altered cDNA sequence snippet AGTACAAGCGCCAGGCACAGACTGACCGAGTGAGCCTGCGG
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQTDRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
speed 1.17 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