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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: ENST00000291582
MT speed 1.02 s - this script 3.118266 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
AIREdisease_causing_automatic0.999961092417917simple_aaeaffected0K83Esingle base exchangers121434255show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999961092417917 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970073)
  • known disease mutation: rs3308 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:45706554A>GN/A show variant in all transcripts   IGV
HGNC symbol AIRE
Ensembl transcript ID ENST00000291582
Genbank transcript ID NM_000383
UniProt peptide O43918
alteration type single base exchange
alteration region CDS
DNA changes c.247A>G
cDNA.374A>G
g.834A>G
AA changes K83E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 83
frameshift no
known variant Reference ID: rs121434255
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs3308 (pathogenic for Polyglandular autoimmune syndrome, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970073)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970073)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970073)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3150.999
3.6461
(flanking)3.6461
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained8330.72mu: CTGTTCGAGGACTAC GTTC|gagg
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      83TAILDFWRVLFKDYNLERYGRLQP
mutated  all conserved    83TAILDFWRVLFEDYNLERYGRLQ
Ptroglodytes  all identical  ENSPTRG00000013974  83TAILDFWRVLFKDYNLERYGRLQ
Mmulatta  all identical  ENSMMUG00000004168  83TVILDFWRVLFKDYNLERYGRLQ
Fcatus  all identical  ENSFCAG00000007933  39AAILDFWRVLFKDYNLERYARLQ
Mmusculus  all identical  ENSMUSG00000000731  84GAILDFWRILFKDYNLERYSRLH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004715  80SIIRAFWSNLSKDYNLDSYPKLH
Drerio  all identical  ENSDARG00000056784  88TVLKAFWKNLCKEYNKECYPKLE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1105DOMAINHSR.lost
181280DOMAINSAND.might get lost (downstream of altered splice site)
295295MUTAGENN->A: Abolishes interaction with histone H3.might get lost (downstream of altered splice site)
295298REGIONInteraction with histone H3 not methylated at 'Lys-4'.might get lost (downstream of altered splice site)
296343ZN_FINGPHD-type 1.might get lost (downstream of altered splice site)
297297MUTAGEND->A: Strongly reduces interaction with unmethylated histone H3 and abolishes interaction with histone H3 trimethylated at 'Lys-4'.might get lost (downstream of altered splice site)
298298MUTAGENE->A: Reduces interaction with histone H3.might get lost (downstream of altered splice site)
298303STRANDmight get lost (downstream of altered splice site)
302302MUTAGENC->P: Reduces transcriptional activation.might get lost (downstream of altered splice site)
303303MUTAGENR->P: Alters protein folding and abolishes interaction with histone H3.might get lost (downstream of altered splice site)
304304MUTAGEND->A: Strongly reduces interaction with histone H3.might get lost (downstream of altered splice site)
304312REGIONInteraction with histone H3 not methylated at 'Lys-4'.might get lost (downstream of altered splice site)
306310STRANDmight get lost (downstream of altered splice site)
307307MUTAGENE->A: Reduces interaction with histone H3.might get lost (downstream of altered splice site)
312312MUTAGEND->A: Abolishes interaction with histone H3.might get lost (downstream of altered splice site)
312314STRANDmight get lost (downstream of altered splice site)
317319STRANDmight get lost (downstream of altered splice site)
320322TURNmight get lost (downstream of altered splice site)
323325STRANDmight get lost (downstream of altered splice site)
331335REGIONInteraction with histone H3 not methylated at 'Lys-4'.might get lost (downstream of altered splice site)
338342HELIXmight get lost (downstream of altered splice site)
414418MOTIFLXXLL motif 3.might get lost (downstream of altered splice site)
434475ZN_FINGPHD-type 2.might get lost (downstream of altered splice site)
437437MUTAGENC->P: Reduces transcription activation.might get lost (downstream of altered splice site)
437467CONFLICTCGDGTDVLRCTHCAAAFHWRCHFPAGTSRPG -> W (in Ref. 3; CAA08759).might get lost (downstream of altered splice site)
516520MOTIFLXXLL motif 4.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1638 / 1638
position (AA) of stopcodon in wt / mu AA sequence 546 / 546
position of stopcodon in wt / mu cDNA 1765 / 1765
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 128 / 128
chromosome 21
strand 1
last intron/exon boundary 1694
theoretical NMD boundary in CDS 1516
length of CDS 1638
coding sequence (CDS) position 247
cDNA position
(for ins/del: last normal base / first normal base)		 374
gDNA position
(for ins/del: last normal base / first normal base)		 834
chromosomal position
(for ins/del: last normal base / first normal base)		 45706554
original gDNA sequence snippet ACTTCTGGAGGGTGCTGTTCAAGGACTACAACCTGGAGCGC
altered gDNA sequence snippet ACTTCTGGAGGGTGCTGTTCGAGGACTACAACCTGGAGCGC
original cDNA sequence snippet ACTTCTGGAGGGTGCTGTTCAAGGACTACAACCTGGAGCGC
altered cDNA sequence snippet ACTTCTGGAGGGTGCTGTTCGAGGACTACAACCTGGAGCGC
wildtype AA sequence MATDAALRRL LRLHRTEIAV AVDSAFPLLH ALADHDVVPE DKFQETLHLK EKEGCPQAFH
ALLSWLLTQD STAILDFWRV LFKDYNLERY GRLQPILDSF PKDVDLSQPR KGRKPPAVPK
ALVPPPRLPT KRKASEEARA AAPAALTPRG TASPGSQLKA KPPKKPESSA EQQRLPLGNG
IQTMSASVQR AVAMSSGDVP GARGAVEGIL IQQVFESGGS KKCIQVGGEF YTPSKFEDSG
SGKNKARSSS GPKPLVRAKG AQGAAPGGGE ARLGQQGSVP APLALPSDPQ LHQKNEDECA
VCRDGGELIC CDGCPRAFHL ACLSPPLREI PSGTWRCSSC LQATVQEVQP RAEEPRPQEP
PVETPLPPGL RSAGEEVRGP PGEPLAGMDT TLVYKHLPAP PSAAPLPGLD SSALHPLLCV
GPEGQQNLAP GARCGVCGDG TDVLRCTHCA AAFHWRCHFP AGTSRPGTGL RCRSCSGDVT
PAPVEGVLAP SPARLAPGPA KDDTASHEPA LHRDDLESLL SEHTFDGILQ WAIQSMARPA
APFPS*
mutated AA sequence MATDAALRRL LRLHRTEIAV AVDSAFPLLH ALADHDVVPE DKFQETLHLK EKEGCPQAFH
ALLSWLLTQD STAILDFWRV LFEDYNLERY GRLQPILDSF PKDVDLSQPR KGRKPPAVPK
ALVPPPRLPT KRKASEEARA AAPAALTPRG TASPGSQLKA KPPKKPESSA EQQRLPLGNG
IQTMSASVQR AVAMSSGDVP GARGAVEGIL IQQVFESGGS KKCIQVGGEF YTPSKFEDSG
SGKNKARSSS GPKPLVRAKG AQGAAPGGGE ARLGQQGSVP APLALPSDPQ LHQKNEDECA
VCRDGGELIC CDGCPRAFHL ACLSPPLREI PSGTWRCSSC LQATVQEVQP RAEEPRPQEP
PVETPLPPGL RSAGEEVRGP PGEPLAGMDT TLVYKHLPAP PSAAPLPGLD SSALHPLLCV
GPEGQQNLAP GARCGVCGDG TDVLRCTHCA AAFHWRCHFP AGTSRPGTGL RCRSCSGDVT
PAPVEGVLAP SPARLAPGPA KDDTASHEPA LHRDDLESLL SEHTFDGILQ WAIQSMARPA
APFPS*
speed 1.02 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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