Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999996 (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) chr6:31237802A>GN/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.1067T>C
cDNA.1067T>C
g.2106T>C
AA changes V356A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 356
frameshift no
known variant Reference ID: rs1050147
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC28252-237374515
regulatory features 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
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3060
-2.7730
(flanking)0.1230
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased2113wt: 0.3227 / mu: 0.3234 (marginal change - not scored)wt: CTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAGCTGTGGT
mu: CTGGCTGTCCTGGCTGTCCTAGCTGTCCTTGGAGCTGTGGT		 ccta|GCTG
Acc increased2103wt: 0.23 / mu: 0.36wt: CGTTGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTG
mu: CGTTGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTCCTTG		 tcct|GGTT
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      356IMGIVAGLAVLVVLAVLGAVVTAM
mutated  not conserved    356IMGIVAGLAVLAVLAV
Ptroglodytes  not conserved  ENSPTRG00000041261  319IVGIAAGLAVLAVLAV
Mmulatta  not conserved  ENSMMUG00000029841  314IAAIVAG------LIVLG
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 
334366TOPO_DOMCytoplasmic (Potential).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 1067
cDNA position
(for ins/del: last normal base / first normal base)		 1067
gDNA position
(for ins/del: last normal base / first normal base)		 2106
chromosomal position
(for ins/del: last normal base / first normal base)		 31237802
original gDNA sequence snippet TGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAG
altered gDNA sequence snippet TGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTCCTTGGAG
original cDNA sequence snippet TGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAG
altered cDNA sequence snippet TGCTGGCCTGGCTGTCCTGGCTGTCCTAGCTGTCCTTGGAG
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 QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLAVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
speed 0.92 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