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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000412585
MT speed 0 s - this script 4.574331 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-Bpolymorphism_automatic1.15019105351166e-13simple_aaeaffectedV9Lsingle base exchangers1050462show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999885 (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) chr6:31324911C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-B
Ensembl transcript ID ENST00000412585
Genbank transcript ID NM_005514
UniProt peptide P30481
alteration type single base exchange
alteration region CDS
DNA changes c.25G>C
cDNA.54G>C
g.55G>C
AA changes V9L Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS
9
frameshift no
known variant Reference ID: rs1050462
databasehomozygous (G/G)heterozygousallele carriers
1000G1558451000
ExAC23449115145
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 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
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2150.038
0.9570.038
(flanking)0.0090.029
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased66wt: 0.69 / mu: 0.84wt: CCCCGAACCGTCCTCCTGCTGCTCTCGGCGGCCCTGGCCCT
mu: CCCCGAACCCTCCTCCTGCTGCTCTCGGCGGCCCTGGCCCT
 gctg|CTCT
Acc increased64wt: 0.77 / mu: 0.92wt: CGCCCCGAACCGTCCTCCTGCTGCTCTCGGCGGCCCTGGCC
mu: CGCCCCGAACCCTCCTCCTGCTGCTCTCGGCGGCCCTGGCC
 ctgc|TGCT
Acc gained620.57mu: GGCGCCCCGAACCCTCCTCCTGCTGCTCTCGGCGGCCCTGG tcct|GCTG
distance from splice site 49
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MLVMAPRTVLLLLSAALALTE
mutated  all conserved    9 MLVMAPRTLLLLLSAALALTET
Ptroglodytes  all identical  ENSPTRG00000038986  9 MQVTAPRTVLLLLSAALALTET
Mmulatta  all conserved  ENSMMUG00000029841  9 ILAPRTLLLLLSGALALTET
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)
25309TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
2736STRANDmight get lost (downstream of altered splice site)
4143STRANDmight get lost (downstream of altered splice site)
4552STRANDmight get lost (downstream of altered splice site)
5561STRANDmight get lost (downstream of altered splice site)
6466STRANDmight get lost (downstream of altered splice site)
7476HELIXmight get lost (downstream of altered splice site)
81108HELIXmight get lost (downstream of altered splice site)
106106CONFLICTL -> A (in Ref. 12; AAA59619).might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...) (By similarity).might get lost (downstream of altered splice site)
113115STRANDmight get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
118127STRANDmight get lost (downstream of altered splice site)
125125DISULFIDmight get lost (downstream of altered splice site)
129132STRANDmight get lost (downstream of altered splice site)
133142STRANDmight get lost (downstream of altered splice site)
145150STRANDmight get lost (downstream of altered splice site)
157161STRANDmight get lost (downstream of altered splice site)
162173HELIXmight get lost (downstream of altered splice site)
176185HELIXmight get lost (downstream of altered splice site)
187198HELIXmight get lost (downstream of altered splice site)
188188DISULFIDmight get lost (downstream of altered splice site)
200203HELIXmight 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)
210219STRANDmight get lost (downstream of altered splice site)
222235STRANDmight get lost (downstream of altered splice site)
223223CONFLICTV -> A (in Ref. 12; AAA59619).might get lost (downstream of altered splice site)
227227DISULFIDmight get lost (downstream of altered splice site)
229229CONFLICTA -> S (in Ref. 12; AAA59619).might get lost (downstream of altered splice site)
238243STRANDmight get lost (downstream of altered splice site)
249251HELIXmight get lost (downstream of altered splice site)
252254STRANDmight get lost (downstream of altered splice site)
261263STRANDmight get lost (downstream of altered splice site)
265274STRANDmight get lost (downstream of altered splice site)
278280HELIXmight get lost (downstream of altered splice site)
281286STRANDmight get lost (downstream of altered splice site)
283283DISULFIDmight get lost (downstream of altered splice site)
290292STRANDmight get lost (downstream of altered splice site)
294296STRANDmight get lost (downstream of altered splice site)
299309REGIONConnecting peptide.might get lost (downstream of altered splice site)
310333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334362TOPO_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 1089 / 1089
position (AA) of stopcodon in wt / mu AA sequence 363 / 363
position of stopcodon in wt / mu cDNA 1118 / 1118
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 30 / 30
chromosome 6
strand -1
last intron/exon boundary 1123
theoretical NMD boundary in CDS 1043
length of CDS 1089
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)
54
gDNA position
(for ins/del: last normal base / first normal base)
55
chromosomal position
(for ins/del: last normal base / first normal base)
31324911
original gDNA sequence snippet TGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCTCGGCG
altered gDNA sequence snippet TGGTCATGGCGCCCCGAACCCTCCTCCTGCTGCTCTCGGCG
original cDNA sequence snippet TGGTCATGGCGCCCCGAACCGTCCTCCTGCTGCTCTCGGCG
altered cDNA sequence snippet TGGTCATGGCGCCCCGAACCCTCCTCCTGCTGCTCTCGGCG
wildtype AA sequence MLVMAPRTVL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPREE PRAPWIEQEG PEYWDRNTQI YKAQAQTDRE SLRNLRGYYN QSEAGSHTLQ
SMYGCDVGPD GRLLRGHDQY AYDGKDYIAL NEDLRSWTAA DTAAQITQRK WEAAREAEQR
RAYLEGECVE WLRRYLENGK DKLERADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP
SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL
TA*
mutated AA sequence MLVMAPRTLL LLLSAALALT ETWAGSHSMR YFYTSVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPREE PRAPWIEQEG PEYWDRNTQI YKAQAQTDRE SLRNLRGYYN QSEAGSHTLQ
SMYGCDVGPD GRLLRGHDQY AYDGKDYIAL NEDLRSWTAA DTAAQITQRK WEAAREAEQR
RAYLEGECVE WLRRYLENGK DKLERADPPK THVTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDRTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEP
SSQSTVPIVG IVAGLAVLAV VVIGAVVAAV MCRRKSSGGK GGSYSQAACS DSAQGSDVSL
TA*
speed 1.61 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
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Problems