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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: ENST00000328698
MT speed 0.75 s - this script 2.800944 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DEFB108Bpolymorphism_automatic0.000178779027278031simple_aaeaffectedR36Wsingle base exchangers12793731show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999821220972722 (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) chr11:71548492C>TN/A show variant in all transcripts   IGV
HGNC symbol DEFB108B
Ensembl transcript ID ENST00000328698
Genbank transcript ID NM_001002035
UniProt peptide Q8NET1
alteration type single base exchange
alteration region CDS
DNA changes c.106C>T
cDNA.106C>T
g.4247C>T
AA changes R36W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
36
frameshift no
known variant Reference ID: rs12793731
databasehomozygous (T/T)heterozygousallele carriers
1000G3128121124
ExAC11947887320820
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.20.634
1.1530.509
(flanking)-0.3070.124
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4258wt: 0.35 / mu: 0.49wt: GGCTCCTGTCGGGACTTTTGCCTTGAAACAGAAATCCATGT
mu: GGCTCCTGTTGGGACTTTTGCCTTGAAACAGAAATCCATGT
 ttgc|CTTG
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      36KEICERPNGSCRDFCLETEIHVGR
mutated  not conserved    36KEICERPNGSCWDFCLETEIHVG
Ptroglodytes  all identical  ENSPTRG00000034221  36KEICERPNGSCRDFCLETEIHVR
Mmulatta  all identical  ENSMMUG00000017578  36KEICERPNGSCRDFCLKTEIHVG
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 
2373PEPTIDEBeta-defensin 108B. /FTId=PRO_0000006981.lost
3939DISULFIDBy similarity.might get lost (downstream of altered splice site)
4949DISULFIDBy similarity.might get lost (downstream of altered splice site)
5555DISULFIDBy similarity.might get lost (downstream of altered splice site)
5656DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 222 / 222
position (AA) of stopcodon in wt / mu AA sequence 74 / 74
position of stopcodon in wt / mu cDNA 222 / 222
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 11
strand 1
last intron/exon boundary 59
theoretical NMD boundary in CDS 8
length of CDS 222
coding sequence (CDS) position 106
cDNA position
(for ins/del: last normal base / first normal base)
106
gDNA position
(for ins/del: last normal base / first normal base)
4247
chromosomal position
(for ins/del: last normal base / first normal base)
71548492
original gDNA sequence snippet AACGTCCAAATGGCTCCTGTCGGGACTTTTGCCTTGAAACA
altered gDNA sequence snippet AACGTCCAAATGGCTCCTGTTGGGACTTTTGCCTTGAAACA
original cDNA sequence snippet AACGTCCAAATGGCTCCTGTCGGGACTTTTGCCTTGAAACA
altered cDNA sequence snippet AACGTCCAAATGGCTCCTGTTGGGACTTTTGCCTTGAAACA
wildtype AA sequence MRIAVLLFAI FFFMSQVLPA RGKFKEICER PNGSCRDFCL ETEIHVGRCL NSQPCCLPLG
HQPRIESTTP KKD*
mutated AA sequence MRIAVLLFAI FFFMSQVLPA RGKFKEICER PNGSCWDFCL ETEIHVGRCL NSQPCCLPLG
HQPRIESTTP KKD*
speed 0.75 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