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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: ENST00000264926
MT speed 1.24 s - this script 4.90475 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
RAD18polymorphism_automatic8.17249215967486e-07simple_aaeaffectedR302Qsingle base exchangers373572show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999182750784 (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) chr3:8955389C>TN/A show variant in all transcripts   IGV
HGNC symbol RAD18
Ensembl transcript ID ENST00000264926
Genbank transcript ID NM_020165
UniProt peptide Q9NS91
alteration type single base exchange
alteration region CDS
DNA changes c.905G>A
cDNA.1022G>A
g.50069G>A
AA changes R302Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
302
frameshift no
known variant Reference ID: rs373572
databasehomozygous (T/T)heterozygousallele carriers
1000G11239972120
ExAC28693-246194074
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0951
1.0911
(flanking)0.2491
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased50065wt: 0.56 / mu: 0.92wt: AAATAGTTCGAGAAA
mu: AAATAGTTCAAGAAA
 ATAG|ttcg
Donor increased50070wt: 0.58 / mu: 0.80wt: GTTCGAGAAATCGAA
mu: GTTCAAGAAATCGAA
 TCGA|gaaa
Donor gained500690.43mu: AGTTCAAGAAATCGA TTCA|agaa
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      302ALHPKSAAEIVREIENIEKTRMRL
mutated  all conserved    302VQEIENIEKTRMR
Ptroglodytes  all conserved  ENSPTRG00000014583  302VQEIENMEKTRMR
Mmulatta  all conserved  ENSMMUG00000020013  301VQEIENMEKTRMR
Fcatus  no alignment  ENSFCAG00000008875  n/a
Mmusculus  all conserved  ENSMUSG00000030254  302VQEIESMEKTRMR
Ggallus  all conserved  ENSGALG00000008368  309LNPKSVAEIVKELAKNEKIRVQ
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000027938  297AEEIAKEVEANERLKNQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
322322MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
342345HELIXmight get lost (downstream of altered splice site)
347358HELIXmight get lost (downstream of altered splice site)
403403MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
409409MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
471471MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
482484CONFLICTESA -> GKC (in Ref. 2; AAF80856).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1488 / 1488
position (AA) of stopcodon in wt / mu AA sequence 496 / 496
position of stopcodon in wt / mu cDNA 1605 / 1605
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 118 / 118
chromosome 3
strand -1
last intron/exon boundary 1503
theoretical NMD boundary in CDS 1335
length of CDS 1488
coding sequence (CDS) position 905
cDNA position
(for ins/del: last normal base / first normal base)
1022
gDNA position
(for ins/del: last normal base / first normal base)
50069
chromosomal position
(for ins/del: last normal base / first normal base)
8955389
original gDNA sequence snippet AACAGCTGCTGAAATAGTTCGAGAAATCGAAAATATAGAGA
altered gDNA sequence snippet AACAGCTGCTGAAATAGTTCAAGAAATCGAAAATATAGAGA
original cDNA sequence snippet ATCAGCTGCTGAAATAGTTCGAGAAATCGAAAATATAGAGA
altered cDNA sequence snippet ATCAGCTGCTGAAATAGTTCAAGAAATCGAAAATATAGAGA
wildtype AA sequence MDSLAESRWP PGLAVMKTID DLLRCGICFE YFNIAMIIPQ CSHNYCSLCI RKFLSYKTQC
PTCCVTVTEP DLKNNRILDE LVKSLNFARN HLLQFALESP AKSPASSSSK NLAVKVYTPV
ASRQSLKQGS RLMDNFLIRE MSGSTSELLI KENKSKFSPQ KEASPAAKTK ETRSVEEIAP
DPSEAKRPEP PSTSTLKQVT KVDCPVCGVN IPESHINKHL DSCLSREEKK ESLRSSVHKR
KPLPKTVYNL LSDRDLKKKL KEHGLSIQGN KQQLIKRHQE FVHMYNAQCD ALHPKSAAEI
VREIENIEKT RMRLEASKLN ESVMVFTKDQ TEKEIDEIHS KYRKKHKSEF QLLVDQARKG
YKKIAGMSQK TVTITKEDES TEKLSSVCMG QEDNMTSVTN HFSQSKLDSP EELEPDREED
SSSCIDIQEV LSSSESDSCN SSSSDIIRDL LEEEEAWEAS HKNDLQDTEI SPRQNRRTRA
AESAEIEPRN KRNRN*
mutated AA sequence MDSLAESRWP PGLAVMKTID DLLRCGICFE YFNIAMIIPQ CSHNYCSLCI RKFLSYKTQC
PTCCVTVTEP DLKNNRILDE LVKSLNFARN HLLQFALESP AKSPASSSSK NLAVKVYTPV
ASRQSLKQGS RLMDNFLIRE MSGSTSELLI KENKSKFSPQ KEASPAAKTK ETRSVEEIAP
DPSEAKRPEP PSTSTLKQVT KVDCPVCGVN IPESHINKHL DSCLSREEKK ESLRSSVHKR
KPLPKTVYNL LSDRDLKKKL KEHGLSIQGN KQQLIKRHQE FVHMYNAQCD ALHPKSAAEI
VQEIENIEKT RMRLEASKLN ESVMVFTKDQ TEKEIDEIHS KYRKKHKSEF QLLVDQARKG
YKKIAGMSQK TVTITKEDES TEKLSSVCMG QEDNMTSVTN HFSQSKLDSP EELEPDREED
SSSCIDIQEV LSSSESDSCN SSSSDIIRDL LEEEEAWEAS HKNDLQDTEI SPRQNRRTRA
AESAEIEPRN KRNRN*
speed 1.24 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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