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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: ENST00000325995
MT speed 0 s - this script 2.975533 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
KLHL38polymorphism_automatic1.44195766438315e-12simple_aaeaffectedR346Ksingle base exchangers11780509show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998558 (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) chr8:124664130C>TN/A show variant in all transcripts   IGV
HGNC symbol KLHL38
Ensembl transcript ID ENST00000325995
Genbank transcript ID NM_001081675
UniProt peptide Q2WGJ6
alteration type single base exchange
alteration region CDS
DNA changes c.1037G>A
cDNA.1061G>A
g.1061G>A
AA changes R346K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 346
frameshift no
known variant Reference ID: rs11780509
databasehomozygous (T/T)heterozygousallele carriers
1000G125810242282
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.730.046
0.340.006
(flanking)0.7760.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1063wt: 0.47 / mu: 0.85wt: GGAGGAGTCTGGTCA
mu: GGAAGAGTCTGGTCA		 AGGA|gtct
Donor marginally increased1056wt: 0.9589 / mu: 0.9984 (marginal change - not scored)wt: AGCTCAGGGAGGAGT
mu: AGCTCAGGGAAGAGT		 CTCA|ggga
distance from splice site 314
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      346YVLGGMAVSSGRSLVSHNVYIFSL
mutated  all conserved    346YVLGGMAVSSGKSLVSHNVYIFS
Ptroglodytes  all identical  ENSPTRG00000020556  345YVLGGMAVSSGRSLVSHNVYIFS
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000022357  346YVLGGMTVSEGKSLISCGVYIFS
Ggallus  all conserved  ENSGALG00000016368  346YVLGGMPVSNKKSPVSDNIYIYS
Trubripes  all conserved  ENSTRUG00000005434  369YVLGGLTTNTEQAQVSTSVYTLS
Drerio  not conserved  ENSDARG00000031383  346YVVGGLSLSLVSGDSAVSATVYTLS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
334383REPEATKelch 2.lost
384431REPEATKelch 3.might get lost (downstream of altered splice site)
433479REPEATKelch 4.might get lost (downstream of altered splice site)
480521REPEATKelch 5.might get lost (downstream of altered splice site)
523573REPEATKelch 6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1746 / 1746
position (AA) of stopcodon in wt / mu AA sequence 582 / 582
position of stopcodon in wt / mu cDNA 1770 / 1770
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 25 / 25
chromosome 8
strand -1
last intron/exon boundary 1481
theoretical NMD boundary in CDS 1406
length of CDS 1746
coding sequence (CDS) position 1037
cDNA position
(for ins/del: last normal base / first normal base)		 1061
gDNA position
(for ins/del: last normal base / first normal base)		 1061
chromosomal position
(for ins/del: last normal base / first normal base)		 124664130
original gDNA sequence snippet CATGGCTGTCAGCTCAGGGAGGAGTCTGGTCAGTCACAATG
altered gDNA sequence snippet CATGGCTGTCAGCTCAGGGAAGAGTCTGGTCAGTCACAATG
original cDNA sequence snippet CATGGCTGTCAGCTCAGGGAGGAGTCTGGTCAGTCACAATG
altered cDNA sequence snippet CATGGCTGTCAGCTCAGGGAAGAGTCTGGTCAGTCACAATG
wildtype AA sequence MDEESLDGLL FKDHDFSSDL LRQLNSLRQS RILTDVSICA GAREIPCHRN VLASSSPYFR
AMFCSSFREK SEAKVQLKGI DPPTLDQIVS YVYTGEAHIA TDNVLPVMEA ASMLQFPKLF
EACSSYLQSQ LAPSNCLGMI RLSEILSCET LKKKAREVAL TSFPEVAASA DLKELCALEL
RDYLGDDGLC GEEEKVFEAL MVWIKHDLQA RKRYMQELFK QVRLQYIHPA FFHHFIANDA
LLQSSPACQI ILETAKRQMF SLCGTTVPDC KLLLHVPPRN SYQDFLILLG GRKDSQQTTR
DVLLYSKQTG QWQSLAKLPT RLYKASAITL HRSIYVLGGM AVSSGRSLVS HNVYIFSLKL
NQWRLGEPML VARYSHRSTA HKNFIFSIGG IGEGQELMGS MERYDSICNV WESMASMPVG
VLHPAVAVKD QRLYLFGGED IMQNPVRLIQ VYHISRNSWF KMETRMIKNV CAPAVVLGER
IVIVGGYTRR ILAYDPQSNK FVKCADMKDR RMHHGATVMG NKLYVTGGRR LTTDCNIEDS
ASFDCYDPET DTWTSQGQLP HKLFDHACLT LQCIPRTSGL P*
mutated AA sequence MDEESLDGLL FKDHDFSSDL LRQLNSLRQS RILTDVSICA GAREIPCHRN VLASSSPYFR
AMFCSSFREK SEAKVQLKGI DPPTLDQIVS YVYTGEAHIA TDNVLPVMEA ASMLQFPKLF
EACSSYLQSQ LAPSNCLGMI RLSEILSCET LKKKAREVAL TSFPEVAASA DLKELCALEL
RDYLGDDGLC GEEEKVFEAL MVWIKHDLQA RKRYMQELFK QVRLQYIHPA FFHHFIANDA
LLQSSPACQI ILETAKRQMF SLCGTTVPDC KLLLHVPPRN SYQDFLILLG GRKDSQQTTR
DVLLYSKQTG QWQSLAKLPT RLYKASAITL HRSIYVLGGM AVSSGKSLVS HNVYIFSLKL
NQWRLGEPML VARYSHRSTA HKNFIFSIGG IGEGQELMGS MERYDSICNV WESMASMPVG
VLHPAVAVKD QRLYLFGGED IMQNPVRLIQ VYHISRNSWF KMETRMIKNV CAPAVVLGER
IVIVGGYTRR ILAYDPQSNK FVKCADMKDR RMHHGATVMG NKLYVTGGRR LTTDCNIEDS
ASFDCYDPET DTWTSQGQLP HKLFDHACLT LQCIPRTSGL P*
speed 0.82 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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