Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999871 (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 ENST00000376228
Genbank transcript ID NM_002117
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.853A>G
cDNA.868A>G
g.1879A>G
AA changes M285V Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 285
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      285PSGQEQRYTCHMQHEGLQEPLTLS
mutated  all conserved    285PSGQEQRYTCHVQHEGLQEPLTL
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 
25308TOPO_DOMExtracellular (Potential).lost
207298REGIONAlpha-3.lost
209297DOMAINIg-like C1-type.lost
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 1101 / 1101
position (AA) of stopcodon in wt / mu AA sequence 367 / 367
position of stopcodon in wt / mu cDNA 1116 / 1116
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 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1112
theoretical NMD boundary in CDS 1046
length of CDS 1101
coding sequence (CDS) position 853
cDNA position
(for ins/del: last normal base / first normal base)		 868
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 ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES
LITCKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHVQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES
LITCKA*
speed 1.01 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