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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 3.051642 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BRAFdisease_causing_automatic0.999999966119932simple_aaeaffected0Q257Rsingle base exchangers180177035show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999966119932 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM060874)
  • known disease mutation: rs13973 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:140501302T>CN/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.770A>G
cDNA.831A>G
g.123263A>G
AA changes Q257R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs180177035
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13973 (pathogenic for Cardiofaciocutaneous syndrome 1|Noonan syndrome 7|LEOPARD syndrome 3|Cardio-facio-cutaneous syndrome|Rasopathy|Inborn genetic diseases|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060874)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060874)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060874)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3930.999
5.0051
(flanking)6.0591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased123273wt: 0.23 / mu: 0.36wt: CTGCTTTTCCAGGGTTTCCGCTGTCAAACATGTGGTTATAA
mu: CTGCTTTTCCGGGGTTTCCGCTGTCAAACATGTGGTTATAA		 ccgc|TGTC
Acc increased123262wt: 0.40 / mu: 0.64wt: TTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGCTGTCAAACA
mu: TTTGTCGAAAGCTGCTTTTCCGGGGTTTCCGCTGTCAAACA		 ttcc|AGGG
Acc increased123271wt: 0.26 / mu: 0.38wt: AGCTGCTTTTCCAGGGTTTCCGCTGTCAAACATGTGGTTAT
mu: AGCTGCTTTTCCGGGGTTTCCGCTGTCAAACATGTGGTTAT		 ttcc|GCTG
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257AFCDFCRKLLFQGFRCQTCGYKFH
mutated  all conserved    257AFCDFCRKLLFRGFRCQTCGYKF
Ptroglodytes  all identical  ENSPTRG00000019769  257AFCDFCRKLLFQGFRCQTCGYKF
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000012847  177AFCDFCGKLFFQG
Mmusculus  all identical  ENSMUSG00000002413  241AFCDFCRKLLFQGFRCQTCGYKF
Ggallus  all identical  ENSGALG00000012865  211AFCDFCRKLLFQGFRCQTCGYKF
Trubripes  all identical  ENSTRUG00000011625  267AFCDFCRKLLFQGFRCQTCGYKF
Drerio  all identical  ENSDARG00000017661  267AFCDFCRKLLFQGFRCQTCGYKF
Dmelanogaster  not conserved  FBgn0003079  285VFCEGCRRLLFTGFYCSQCNFRF
Celegans  not conserved  Y73B6A.5  193WMMGFRCEFCQFKF
Xtropicalis  all identical  ENSXETG00000004845  242RKLLFQGFRCQTCGYKF
protein features
start (aa)end (aa)featuredetails 
234280ZN_FINGPhorbol-ester/DAG-type.lost
261261METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
264264METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
269269METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
272272METALZinc 2 (By similarity).might get lost (downstream of altered splice site)
280280METALZinc 1 (By similarity).might get lost (downstream of altered splice site)
365365MOD_RESPhosphoserine; by SGK1.might get lost (downstream of altered splice site)
373373MOD_RESPhosphothreonine; by autocatalysis.might get lost (downstream of altered splice site)
380381SITEBreakpoint for translocation to form KIAA1549-BRAF fusion protein.might get lost (downstream of altered splice site)
396396MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
399399MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
401401MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
418418MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
419419MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
428432COMPBIASPoly-Ser.might get lost (downstream of altered splice site)
438439SITEBreakpoint for translocation to form KIAA1549-BRAF fusion protein.might get lost (downstream of altered splice site)
446446MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
447447MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
457717DOMAINProtein kinase.might get lost (downstream of altered splice site)
458464STRANDmight get lost (downstream of altered splice site)
463471NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
465465MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
466468STRANDmight get lost (downstream of altered splice site)
470472STRANDmight get lost (downstream of altered splice site)
475484STRANDmight get lost (downstream of altered splice site)
483483BINDINGATP (By similarity).might get lost (downstream of altered splice site)
487489STRANDmight get lost (downstream of altered splice site)
492505HELIXmight get lost (downstream of altered splice site)
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)
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 770
cDNA position
(for ins/del: last normal base / first normal base)		 831
gDNA position
(for ins/del: last normal base / first normal base)		 123263
chromosomal position
(for ins/del: last normal base / first normal base)		 140501302
original gDNA sequence snippet TTGTCGAAAGCTGCTTTTCCAGGGTTTCCGCTGTCAAACAT
altered gDNA sequence snippet TTGTCGAAAGCTGCTTTTCCGGGGTTTCCGCTGTCAAACAT
original cDNA sequence snippet TTGTCGAAAGCTGCTTTTCCAGGGTTTCCGCTGTCAAACAT
altered cDNA sequence snippet TTGTCGAAAGCTGCTTTTCCGGGGTTTCCGCTGTCAAACAT
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 CRKLLFRGFR 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*
speed 0.98 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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