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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: ENST00000541917
MT speed 1.56 s - this script 5.98802 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KIAA2012polymorphism_automatic5.72449865288149e-11simple_aaeV42Asingle base exchangers10221698show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999942755 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:202939654T>CN/A show variant in all transcripts   IGV
HGNC symbol KIAA2012
Ensembl transcript ID ENST00000541917
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region CDS
DNA changes c.125T>C
cDNA.498T>C
g.1677T>C
AA changes V42A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
42
frameshift no
known variant Reference ID: rs10221698
databasehomozygous (C/C)heterozygousallele carriers
1000G3459981343
ExAC175541045859
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8170.013
-0.0760.004
(flanking)1.4710.008
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 increased1679wt: 0.9658 / mu: 0.9714 (marginal change - not scored)wt: CTGTCAGCAAACCTC
mu: CTGCCAGCAAACCTC
 GTCA|gcaa
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42LNWRSPEDYVPVSKPQDKNNASQH
mutated  not conserved    42LNWRSPEDYVPASKPQDKNNASQ
Ptroglodytes  all identical  ENSPTRG00000012814  42LNWRSPEDYVPVSKPQDKNNASQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000047361  43LNWKSPEDYILVSKAQNGDSASQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features N/A
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2010 / 2010
position (AA) of stopcodon in wt / mu AA sequence 670 / 670
position of stopcodon in wt / mu cDNA 2383 / 2383
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 374 / 374
chromosome 2
strand 1
last intron/exon boundary 2474
theoretical NMD boundary in CDS 2050
length of CDS 2010
coding sequence (CDS) position 125
cDNA position
(for ins/del: last normal base / first normal base)
498
gDNA position
(for ins/del: last normal base / first normal base)
1677
chromosomal position
(for ins/del: last normal base / first normal base)
202939654
original gDNA sequence snippet CCCAGAAGACTATGTTCCTGTCAGCAAACCTCAAGATAAGA
altered gDNA sequence snippet CCCAGAAGACTATGTTCCTGCCAGCAAACCTCAAGATAAGA
original cDNA sequence snippet CCCAGAAGACTATGTTCCTGTCAGCAAACCTCAAGATAAGA
altered cDNA sequence snippet CCCAGAAGACTATGTTCCTGCCAGCAAACCTCAAGATAAGA
wildtype AA sequence MFTLSLLSRG HGKLGQDKQK LEVYFEPEDY LNWRSPEDYV PVSKPQDKNN ASQHSWSLFL
PKTFSTRKGA LILYSEGFAI SAWTPKERRK GPYCPRGPWR KLDLELHTLQ DLKEAILAYG
RQQGEQDRAW QPYLHFRSQL ESQAQRQIQP GHSAKRYLRG LLRTWPPDAM YRLWCAGYIK
DSVLLQDSQL NVPKKLRPQQ DLSGVPPKYH LLPVFPSFWI QQGKSFEQRQ QGLDEGEAGA
AGHVDQGPLA KNHGSQGTRL PPRRKQPWQE DETQAEDTSI ENHLCLYASK ESYNEKTQQT
SRKAFGHGRI DHSWLPSDKS HITFCGGAFP NRKADLSDKQ RNVKLHKARS SHLLQVLPAE
RSLFPPVASA TGSRIITPGE VKKKKAPKAL KLPPISEEPP RVLEPLKSQF KANEPPTELF
ILPVEIHYHT KQPPKEKAHR RGAPHPESEP ESSEESTPVW RPPLKHASLE TPWELTVHLP
VDASRDTLSP QGSSSLPPAS LGNLTLKGSK ARHTRVHSQG KGVWKGDDDA PPHDVAPPLD
LLPPIKGKKS PESQKGVDSP RTSDHNSPPS LPNMRVPRRA LPAAQEDSSD PTLGHFLLGP
DGEKVCLSLP GHTQTEALPS GKAYESVNSN ISHEEEGPSS QHFLKDMAAA ASDQGKDDDL
ETFSPKNSL*
mutated AA sequence MFTLSLLSRG HGKLGQDKQK LEVYFEPEDY LNWRSPEDYV PASKPQDKNN ASQHSWSLFL
PKTFSTRKGA LILYSEGFAI SAWTPKERRK GPYCPRGPWR KLDLELHTLQ DLKEAILAYG
RQQGEQDRAW QPYLHFRSQL ESQAQRQIQP GHSAKRYLRG LLRTWPPDAM YRLWCAGYIK
DSVLLQDSQL NVPKKLRPQQ DLSGVPPKYH LLPVFPSFWI QQGKSFEQRQ QGLDEGEAGA
AGHVDQGPLA KNHGSQGTRL PPRRKQPWQE DETQAEDTSI ENHLCLYASK ESYNEKTQQT
SRKAFGHGRI DHSWLPSDKS HITFCGGAFP NRKADLSDKQ RNVKLHKARS SHLLQVLPAE
RSLFPPVASA TGSRIITPGE VKKKKAPKAL KLPPISEEPP RVLEPLKSQF KANEPPTELF
ILPVEIHYHT KQPPKEKAHR RGAPHPESEP ESSEESTPVW RPPLKHASLE TPWELTVHLP
VDASRDTLSP QGSSSLPPAS LGNLTLKGSK ARHTRVHSQG KGVWKGDDDA PPHDVAPPLD
LLPPIKGKKS PESQKGVDSP RTSDHNSPPS LPNMRVPRRA LPAAQEDSSD PTLGHFLLGP
DGEKVCLSLP GHTQTEALPS GKAYESVNSN ISHEEEGPSS QHFLKDMAAA ASDQGKDDDL
ETFSPKNSL*
speed 1.56 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