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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: ENST00000288602
MT speed 1.06 s - this script 5.928377 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BRAFdisease_causing_automatic0.99999999999347simple_aaeaffected0E501Ksingle base exchangers180177038show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.99999999999347 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM060879)
  • known disease mutation: rs13977 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:140477807C>TN/A show variant in all transcripts   IGV
HGNC symbol BRAF
Ensembl transcript ID ENST00000288602
Genbank transcript ID NM_004333
UniProt peptide P15056
alteration type single base exchange
alteration region CDS
DNA changes c.1501G>A
cDNA.1562G>A
g.146758G>A
AA changes E501K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
501
frameshift no
known variant Reference ID: rs180177038
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13977 (pathogenic for Cardiofaciocutaneous syndrome 1|Cardio-facio-cutaneous syndrome|Noonan syndrome|Rasopathy|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060879)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060879)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060879)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7431
5.7461
(flanking)1.6381
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 increased146750wt: 0.4887 / mu: 0.5151 (marginal change - not scored)wt: AGCCTTCAAAAATGA
mu: AGCCTTCAAAAATAA
 CCTT|caaa
Donor marginally increased146755wt: 0.9895 / mu: 0.9903 (marginal change - not scored)wt: TCAAAAATGAAGTAG
mu: TCAAAAATAAAGTAG
 AAAA|atga
Donor gained1467590.42mu: AAATAAAGTAGGAGT ATAA|agta
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      501PTPQQLQAFKNEVGVLRKTRHVNI
mutated  all conserved    501PTPQQLQAFKNKVGVLRKTRHVN
Ptroglodytes  all identical  ENSPTRG00000019769  501PTPQQLQAFKNEVGVLRKTRHVN
Mmulatta  no homologue    
Fcatus  no alignment  ENSFCAG00000012847  n/a
Mmusculus  all identical  ENSMUSG00000002413  538PQQLQAFKNEVGVLRKTRHVN
Ggallus  all identical  ENSGALG00000012865  495PTPQQLQAFKNEVGVLRKTRHVN
Trubripes  all identical  ENSTRUG00000011625  552PTPQQLQAFKNEVGVLRKTRHVN
Drerio  all identical  ENSDARG00000017661  551PTPQQLQAFKNEVGVLRKTRHVN
Dmelanogaster  all identical  FBgn0003079  516PSPAQLQAFKNEVAMLKKTRHCN
Celegans  all identical  Y73B6A.5  525PTPSQMAAFKNEVAVLKKTRHLN
Xtropicalis  all identical  ENSXETG00000004845  526PTPQQLQAFKNEVGVLRK
protein features
start (aa)end (aa)featuredetails 
457717DOMAINProtein kinase.lost
492505HELIXlost
516520STRANDmight get lost (downstream of altered splice site)
522524STRANDmight get lost (downstream of altered splice site)
526530STRANDmight get lost (downstream of altered splice site)
534536STRANDmight get lost (downstream of altered splice site)
537542HELIXmight get lost (downstream of altered splice site)
550569HELIXmight get lost (downstream of altered splice site)
576576ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
579581HELIXmight get lost (downstream of altered splice site)
582585STRANDmight get lost (downstream of altered splice site)
586588TURNmight get lost (downstream of altered splice site)
589592STRANDmight get lost (downstream of altered splice site)
599601STRANDmight get lost (downstream of altered splice site)
614614MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
617619HELIXmight get lost (downstream of altered splice site)
622626HELIXmight get lost (downstream of altered splice site)
629631STRANDmight get lost (downstream of altered splice site)
635651HELIXmight get lost (downstream of altered splice site)
655658TURNmight get lost (downstream of altered splice site)
662671HELIXmight get lost (downstream of altered splice site)
671671MOD_RESOmega-N-methylarginine; by PRMT5.might get lost (downstream of altered splice site)
671671MUTAGENR->K: Increased kinase activity and stability in response to EGF treatment.might get lost (downstream of altered splice site)
678680HELIXmight get lost (downstream of altered splice site)
687696HELIXmight get lost (downstream of altered splice site)
701703HELIXmight get lost (downstream of altered splice site)
707719HELIXmight get lost (downstream of altered splice site)
729729MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
750750MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
753753MOD_RESPhosphothreonine; by MAPK1.might get lost (downstream of altered splice site)
766766CONFLICTH -> D (in Ref. 11; AAA96495).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2301 / 2301
position (AA) of stopcodon in wt / mu AA sequence 767 / 767
position of stopcodon in wt / mu cDNA 2362 / 2362
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 62 / 62
chromosome 7
strand -1
last intron/exon boundary 2189
theoretical NMD boundary in CDS 2077
length of CDS 2301
coding sequence (CDS) position 1501
cDNA position
(for ins/del: last normal base / first normal base)
1562
gDNA position
(for ins/del: last normal base / first normal base)
146758
chromosomal position
(for ins/del: last normal base / first normal base)
140477807
original gDNA sequence snippet AGTTACAAGCCTTCAAAAATGAAGTAGGAGTACTCAGGTGA
altered gDNA sequence snippet AGTTACAAGCCTTCAAAAATAAAGTAGGAGTACTCAGGTGA
original cDNA sequence snippet AGTTACAAGCCTTCAAAAATGAAGTAGGAGTACTCAGGAAA
altered cDNA sequence snippet AGTTACAAGCCTTCAAAAATAAAGTAGGAGTACTCAGGAAA
wildtype AA sequence MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH
IEALLDKFGG EHNPPSIYLE AYEEYTSKLD ALQQREQQLL ESLGNGTDFS VSSSASMDTV
TSSSSSSLSV LPSSLSVFQN PTDVARSNPK SPQKPIVRVF LPNKQRTVVP ARCGVTVRDS
LKKALMMRGL IPECCAVYRI QDGEKKPIGW DTDISWLTGE ELHVEVLENV PLTTHNFVRK
TFFTLAFCDF CRKLLFQGFR CQTCGYKFHQ RCSTEVPLMC VNYDQLDLLF VSKFFEHHPI
PQEEASLAET ALTSGSSPSA PASDSIGPQI LTSPSPSKSI PIPQPFRPAD EDHRNQFGQR
DRSSSAPNVH INTIEPVNID DLIRDQGFRG DGGSTTGLSA TPPASLPGSL TNVKALQKSP
GPQRERKSSS SSEDRNRMKT LGRRDSSDDW EIPDGQITVG QRIGSGSFGT VYKGKWHGDV
AVKMLNVTAP TPQQLQAFKN EVGVLRKTRH VNILLFMGYS TKPQLAIVTQ WCEGSSLYHH
LHIIETKFEM IKLIDIARQT AQGMDYLHAK SIIHRDLKSN NIFLHEDLTV KIGDFGLATV
KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM TGQLPYSNIN
NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK RDERPLFPQI LASIELLARS
LPKIHRSASE PSLNRAGFQT EDFSLYACAS PKTPIQAGGY GAFPVH*
mutated AA sequence MAALSGGGGG GAEPGQALFN GDMEPEAGAG AGAAASSAAD PAIPEEVWNI KQMIKLTQEH
IEALLDKFGG EHNPPSIYLE AYEEYTSKLD ALQQREQQLL ESLGNGTDFS VSSSASMDTV
TSSSSSSLSV LPSSLSVFQN PTDVARSNPK SPQKPIVRVF LPNKQRTVVP ARCGVTVRDS
LKKALMMRGL IPECCAVYRI QDGEKKPIGW DTDISWLTGE ELHVEVLENV PLTTHNFVRK
TFFTLAFCDF CRKLLFQGFR CQTCGYKFHQ RCSTEVPLMC VNYDQLDLLF VSKFFEHHPI
PQEEASLAET ALTSGSSPSA PASDSIGPQI LTSPSPSKSI PIPQPFRPAD EDHRNQFGQR
DRSSSAPNVH INTIEPVNID DLIRDQGFRG DGGSTTGLSA TPPASLPGSL TNVKALQKSP
GPQRERKSSS SSEDRNRMKT LGRRDSSDDW EIPDGQITVG QRIGSGSFGT VYKGKWHGDV
AVKMLNVTAP TPQQLQAFKN KVGVLRKTRH VNILLFMGYS TKPQLAIVTQ WCEGSSLYHH
LHIIETKFEM IKLIDIARQT AQGMDYLHAK SIIHRDLKSN NIFLHEDLTV KIGDFGLATV
KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM TGQLPYSNIN
NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK RDERPLFPQI LASIELLARS
LPKIHRSASE PSLNRAGFQT EDFSLYACAS PKTPIQAGGY GAFPVH*
speed 1.06 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