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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 0 s - this script 3.156155 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BRAFdisease_causing_automatic0.999999984917714simple_aaeaffected0D638Esingle base exchangers180177042show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999984917714 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM062461)
  • known disease mutation at this position (HGMD CM092084)
  • known disease mutation: rs13981 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:140449165A>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.1914T>A
cDNA.1975T>A
g.175400T>A
AA changes D638E Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 638
frameshift no
known variant Reference ID: rs180177042
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13981 (pathogenic for Lung carcinoma|Cardiofaciocutaneous syndrome 1|Noonan syndrome 1|Noonan syndrome 7|LEOPARD syndrome 3|Inborn genetic diseases|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092084)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092084)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092084)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062461)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092084)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.9351
1.0691
(flanking)4.9021
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased175397wt: 0.47 / mu: 0.61wt: CAGTCAGATGTATAT
mu: CAGTCAGAAGTATAT		 GTCA|gatg
Donor increased175395wt: 0.78 / mu: 0.97wt: TTCAGTCAGATGTAT
mu: TTCAGTCAGAAGTAT		 CAGT|caga
Donor marginally increased175393wt: 0.9143 / mu: 0.9206 (marginal change - not scored)wt: CTTTCAGTCAGATGT
mu: CTTTCAGTCAGAAGT		 TTCA|gtca
distance from splice site 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      638MQDKNPYSFQSDVYAFGIVLYELM
mutated  all conserved    638MQDKNPYSFQSEVYAFGIVLYEL
Ptroglodytes  all identical  ENSPTRG00000019769  638MQDKNPYSFQSDVYAFGIVLYEL
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000012847  558MQDKNPYSFQSDVYAFGIVLYEL
Mmusculus  all identical  ENSMUSG00000002413  675MQDKNPYSFQSDVYAFGIVLYEL
Ggallus  all identical  ENSGALG00000012865  632MQDKNPYSFQSDVYAFGIVLYEL
Trubripes  all identical  ENSTRUG00000011625  689LQDKNPYSFQSDVYAFGIVLYEL
Drerio  all identical  ENSDARG00000017661  688LQDKNPYSFQSDVYAFGIVLYEL
Dmelanogaster  all identical  FBgn0003079  653FQSDVYAFGIVMYEL
Celegans  all identical  Y73B6A.5  664MQDDNPYTPQSDV
Xtropicalis  all identical  ENSXETG00000004845  666QDNNPYSFQSDVYAFGIVLYEL
protein features
start (aa)end (aa)featuredetails 
457717DOMAINProtein kinase.lost
635651HELIXlost
655658TURNmight get lost (downstream of altered splice site)
662671HELIXmight 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)
671671MOD_RESOmega-N-methylarginine; by PRMT5.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 1914
cDNA position
(for ins/del: last normal base / first normal base)		 1975
gDNA position
(for ins/del: last normal base / first normal base)		 175400
chromosomal position
(for ins/del: last normal base / first normal base)		 140449165
original gDNA sequence snippet CCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATTGT
altered gDNA sequence snippet CCATACAGCTTTCAGTCAGAAGTATATGCATTTGGAATTGT
original cDNA sequence snippet CCATACAGCTTTCAGTCAGATGTATATGCATTTGGAATTGT
altered cDNA sequence snippet CCATACAGCTTTCAGTCAGAAGTATATGCATTTGGAATTGT
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 EVGVLRKTRH VNILLFMGYS TKPQLAIVTQ WCEGSSLYHH
LHIIETKFEM IKLIDIARQT AQGMDYLHAK SIIHRDLKSN NIFLHEDLTV KIGDFGLATV
KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSEVY AFGIVLYELM TGQLPYSNIN
NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK RDERPLFPQI LASIELLARS
LPKIHRSASE PSLNRAGFQT EDFSLYACAS PKTPIQAGGY GAFPVH*
speed 0.56 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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