MutationTaster - study a chromosomal position

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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 3.114353 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BRAF	disease_causing_automatic	0.999999999999945	simple_aae			0	G534R	single base exchange	rs180177041		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999945 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM062462)
known disease mutation: rs13980 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:140476806C>GN/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.1600G>C
cDNA.1661G>C
g.147759G>C

AA changes

G534R Score: 125 explain score(s)

position(s) of altered AA
if AA alteration in CDS

534

frameshift

known variant

Reference ID: rs180177041
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs13980 (pathogenic for Dandy-Walker syndrome|Tethered cord|Cardiofaciocutaneous syndrome 1|PHACE syndrome|Cardio-facio-cutaneous syndrome|Inborn genetic diseases|Genetic syndrome with a Dandy-Walker malformation as major feature) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM062462)

known disease mutation at this position, please check HGMD for details (HGMD ID CM062462)
known disease mutation at this position, please check HGMD for details (HGMD ID CM062462)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.194	1
	6.194	1
(flanking)	0.506	1

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

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

534

mutated

not conserved

534

Ptroglodytes

all identical

ENSPTRG00000019769

534

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000012847

454

Mmusculus

all identical

ENSMUSG00000002413

571

Ggallus

all identical

ENSGALG00000012865

528

Trubripes

all identical

ENSTRUG00000011625

585

Drerio

all identical

ENSDARG00000017661

584

Dmelanogaster

all identical

FBgn0003079

549

Celegans

all identical

Y73B6A.5

558

EPR

Xtropicalis

all identical

ENSXETG00000004845

562

protein features

start (aa)	end (aa)	feature	details
457	717	DOMAIN	Protein kinase.	lost
534	536	STRAND		lost

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

strand

-1

last intron/exon boundary

2189

theoretical NMD boundary in CDS

2077

length of CDS

2301

coding sequence (CDS) position

1600

cDNA position
(for ins/del: last normal base / first normal base)

1661

gDNA position
(for ins/del: last normal base / first normal base)

147759

chromosomal position
(for ins/del: last normal base / first normal base)

140476806

original gDNA sequence snippet

TTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT

altered gDNA sequence snippet

TTGTTACCCAGTGGTGTGAGCGCTCCAGCTTGTATCACCAT

original cDNA sequence snippet

TTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT

altered cDNA sequence snippet

TTGTTACCCAGTGGTGTGAGCGCTCCAGCTTGTATCACCAT

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 WCERSSLYHH
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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems