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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: ENST00000261623
MT speed 2.29 s - this script 8.336793 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CYBAdisease_causing_automatic0.999991531989215simple_aae0P156Qsingle base exchangers104894515show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.999991531989215 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910096)
  • known disease mutation: rs2260 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88709882G>TN/A show variant in all transcripts   IGV
HGNC symbol CYBA
Ensembl transcript ID ENST00000261623
Genbank transcript ID NM_000101
UniProt peptide P13498
alteration type single base exchange
alteration region CDS
DNA changes c.467C>A
cDNA.606C>A
g.7679C>A
AA changes P156Q Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS
156
frameshift no
known variant Reference ID: rs104894515
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2260 (pathogenic for Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative|Chronic granulomatous disease) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910096)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910096)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910096)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.850.349
3.260.989
(flanking)3.261
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 increased7679wt: 0.9777 / mu: 0.9969 (marginal change - not scored)wt: CCCCCCGCCGCGGCC
mu: CCCCCAGCCGCGGCC
 CCCC|gccg
distance from splice site 98
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156GGTIKQPPSNPPPRPPAEARKKPS
mutated  not conserved    156GGTIKQPPSNPQPRPPAEARKKP
Ptroglodytes  all identical  ENSPTRG00000008458  156GGTIKQPPSNPPPRPPAEARKKP
Mmulatta  all identical  ENSMMUG00000014325  155GGTIKQPPSNPPPRPPAEARKKP
Fcatus  all identical  ENSFCAG00000006655  156GGTIKQPPSNPPPRPPAEARKKS
Mmusculus  all identical  ENSMUSG00000006519  156GGTIKQPPTNPPPRPPAEVRKKP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000018180  156AESIKNPPQNPPPRPPADTRRKR
Drerio  all identical  ENSDARG00000018283  156GESIKEPPQNPPPRPPPELRRKK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017431  156GETIKRPPENPPPRPPAEVRRKQ
protein features
start (aa)end (aa)featuredetails 
133189COMPBIASPro-rich.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 588 / 588
position (AA) of stopcodon in wt / mu AA sequence 196 / 196
position of stopcodon in wt / mu cDNA 727 / 727
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 140 / 140
chromosome 16
strand -1
last intron/exon boundary 509
theoretical NMD boundary in CDS 319
length of CDS 588
coding sequence (CDS) position 467
cDNA position
(for ins/del: last normal base / first normal base)
606
gDNA position
(for ins/del: last normal base / first normal base)
7679
chromosomal position
(for ins/del: last normal base / first normal base)
88709882
original gDNA sequence snippet GCAGCCGCCCAGCAACCCCCCGCCGCGGCCCCCGGCCGAGG
altered gDNA sequence snippet GCAGCCGCCCAGCAACCCCCAGCCGCGGCCCCCGGCCGAGG
original cDNA sequence snippet GCAGCCGCCCAGCAACCCCCCGCCGCGGCCCCCGGCCGAGG
altered cDNA sequence snippet GCAGCCGCCCAGCAACCCCCAGCCGCGGCCCCCGGCCGAGG
wildtype AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPPPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*
mutated AA sequence MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK
KGSTMERWGQ KYMTAVVKLF GPFTRNYYVR AVLHLLLSVP AGFLLATILG TACLAIASGI
YLLAAVRGEQ WTPIEPKPRE RPQIGGTIKQ PPSNPQPRPP AEARKKPSEE EAAVAAGGPP
GGPQVNPIPV TDEVV*
speed 2.29 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