Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999895 (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) chr6:31238029T>CN/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.964A>G
cDNA.964A>G
g.1879A>G
AA changes M322V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 322
frameshift no
known variant Reference ID: rs2308622
databasehomozygous (C/C)heterozygousallele carriers
1000G15537542307
ExAC15163244117604
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5410.111
0.7010.091
(flanking)-0.2370.046
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1873wt: 0.77 / mu: 0.95wt: ACACGTGCCATATGC
mu: ACACGTGCCATGTGC		 ACGT|gcca
Donor gained18780.92mu: TGCCATGTGCAGCAC CCAT|gtgc
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      322PSGQEQRYTCHMQHEGLQEPLTLS
mutated  all conserved    322PSGQEQRYTCHVQHEGLQEPLTL
Ptroglodytes  all conserved  ENSPTRG00000041261  285PSGEEQRYTCHVQHEGLPEPLTL
Mmulatta  all conserved  ENSMMUG00000029841  280PSGEEQRYMCHVQHEGLLEPLTP
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 
309333TRANSMEMHelical; (Potential).lost
334366TOPO_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 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 964
cDNA position
(for ins/del: last normal base / first normal base)		 964
gDNA position
(for ins/del: last normal base / first normal base)		 1879
chromosomal position
(for ins/del: last normal base / first normal base)		 31238029
original gDNA sequence snippet AGCAGAGATACACGTGCCATATGCAGCACGAGGGGCTGCAA
altered gDNA sequence snippet AGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCAA
original cDNA sequence snippet AGCAGAGATACACGTGCCATATGCAGCACGAGGGGCTGCAA
altered cDNA sequence snippet AGCAGAGATACACGTGCCATGTGCAGCACGAGGGGCTGCAA
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 HVQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
speed 0.97 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