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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: ENST00000504209
MT speed 0 s - this script 6.278368 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
USP17L18polymorphism_automatic2.92950108615742e-11simple_aaeS23Psingle base exchangers376110430show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999970705 (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) chr4:9250422T>CN/A show variant in all transcripts   IGV
HGNC symbol USP17L18
Ensembl transcript ID ENST00000504209
Genbank transcript ID NM_001256859
UniProt peptide N/A
alteration type single base exchange
alteration region CDS
DNA changes c.67T>C
cDNA.67T>C
g.67T>C
AA changes S23P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS
23
frameshift no
known variant Reference ID: rs376110430
databasehomozygous (C/C)heterozygousallele carriers
1000G7067931499
ExAC123951
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0340.006
1.0340.005
(flanking)-0.6930.002
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 67
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      23WQFNHFSKLTSSRPDAAFAEIQRT
mutated  not conserved    23WQFNHFSKLTSPRPDAAFAEIQR
Ptroglodytes  all identical  ENSPTRG00000029995  23WQFNHFSKLTSSRPDAAFAEIQR
Mmulatta  all identical  ENSMMUG00000032404  23WQFNHFSKLTSSRPDAAFAEIQR
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000062369  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0260936  n/a
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 1593 / 1593
position (AA) of stopcodon in wt / mu AA sequence 531 / 531
position of stopcodon in wt / mu cDNA 1593 / 1593
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 4
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1593
coding sequence (CDS) position 67
cDNA position
(for ins/del: last normal base / first normal base)
67
gDNA position
(for ins/del: last normal base / first normal base)
67
chromosomal position
(for ins/del: last normal base / first normal base)
9250422
original gDNA sequence snippet ACTTTTCAAAACTCACATCTTCTCGGCCCGATGCAGCTTTT
altered gDNA sequence snippet ACTTTTCAAAACTCACATCTCCTCGGCCCGATGCAGCTTTT
original cDNA sequence snippet ACTTTTCAAAACTCACATCTTCTCGGCCCGATGCAGCTTTT
altered cDNA sequence snippet ACTTTTCAAAACTCACATCTCCTCGGCCCGATGCAGCTTTT
wildtype AA sequence MEDDSLYLGG EWQFNHFSKL TSSRPDAAFA EIQRTSLPEK SPLSCETRVD LCDDLAPVAR
QLAPREKLPL SSRRPAAVGA GLQNMGNTCY VNASLQCLTY TPPLANYMLS REHSQTCHRH
KGCMLCTMQA HITRALHNPG HVIQPSQALA AGFHRGKQED AHEFLMFTVD AMKKACLPGH
KQVDHHSKDT TLIHQIFGGY WRSQIKCLHC HGISDTFDPY LDIALDIQAA QSVQQALEQL
VKPEELNGEN AYHCGVCLQR APASKTLTLH TSAKVLILVL KRFSDVTGNK IAKNVQYPEC
LDMQPYMSQT NTGPLVYVLY AVLVHAGWSC HNGHYFSYVK AQEGQWYKMD DAEVTASSIT
SVLSQQAYVL FYIQKSEWER HSESVSRGRE PRALGAEDTD RRAKQGELKR DHPCLQAPEL
DEHLVERATQ ESTLDHWKFL QEQNKTKPEF NVRKVEGTLP PDVLVIHQSK YKCGMKNHHP
EQQSSLLNLS STTPTHQESM NTGTLASLRG RARRSKGKNK HSKRALLVCQ *
mutated AA sequence MEDDSLYLGG EWQFNHFSKL TSPRPDAAFA EIQRTSLPEK SPLSCETRVD LCDDLAPVAR
QLAPREKLPL SSRRPAAVGA GLQNMGNTCY VNASLQCLTY TPPLANYMLS REHSQTCHRH
KGCMLCTMQA HITRALHNPG HVIQPSQALA AGFHRGKQED AHEFLMFTVD AMKKACLPGH
KQVDHHSKDT TLIHQIFGGY WRSQIKCLHC HGISDTFDPY LDIALDIQAA QSVQQALEQL
VKPEELNGEN AYHCGVCLQR APASKTLTLH TSAKVLILVL KRFSDVTGNK IAKNVQYPEC
LDMQPYMSQT NTGPLVYVLY AVLVHAGWSC HNGHYFSYVK AQEGQWYKMD DAEVTASSIT
SVLSQQAYVL FYIQKSEWER HSESVSRGRE PRALGAEDTD RRAKQGELKR DHPCLQAPEL
DEHLVERATQ ESTLDHWKFL QEQNKTKPEF NVRKVEGTLP PDVLVIHQSK YKCGMKNHHP
EQQSSLLNLS STTPTHQESM NTGTLASLRG RARRSKGKNK HSKRALLVCQ *
speed 1.72 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