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 0 s - this script 2.718624 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BRAF	disease_causing_automatic	0.999999999863303	simple_aae		affected	0	N581D	single base exchange	rs180177040		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999863303 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM060878)
known disease mutation: rs13979 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:140453987T>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.1741A>G
cDNA.1802A>G
g.170578A>G

AA changes

N581D Score: 23 explain score(s)

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

581

frameshift

known variant

Reference ID: rs180177040
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13979 (pathogenic for Cardiofaciocutaneous syndrome 1|Cardio-facio-cutaneous syndrome|Rasopathy|Inborn genetic diseases|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060878)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060878)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060878)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.657	1
	4.872	1
(flanking)	2.182	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	170578	sequence motif lost	-	wt: AATA\|gtat mu: AATG.gtat
Donor increased	170572	wt: 0.79 / mu: 1.00	wt: TCAAGAGTAATAGTA mu: TCAAGAGTAATGGTA	AAGA\|gtaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

581

mutated

all conserved

581

Ptroglodytes

all identical

ENSPTRG00000019769

581

Mmulatta

no homologue

Fcatus

not conserved

ENSFCAG00000012847

501

Mmusculus

all identical

ENSMUSG00000002413

618

Ggallus

all identical

ENSGALG00000012865

575

Trubripes

all identical

ENSTRUG00000011625

632

Drerio

all identical

ENSDARG00000017661

631

Dmelanogaster

all identical

FBgn0003079

596

Celegans

all identical

Y73B6A.5

605

Xtropicalis

all identical

ENSXETG00000004845

609

protein features

start (aa)	end (aa)	feature	details
457	717	DOMAIN	Protein kinase.	lost
579	581	HELIX		lost
582	585	STRAND		might get lost (downstream of altered splice site)
586	588	TURN		might get lost (downstream of altered splice site)
589	592	STRAND		might get lost (downstream of altered splice site)
599	601	STRAND		might get lost (downstream of altered splice site)
614	614	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
617	619	HELIX		might get lost (downstream of altered splice site)
622	626	HELIX		might get lost (downstream of altered splice site)
629	631	STRAND		might get lost (downstream of altered splice site)
635	651	HELIX		might get lost (downstream of altered splice site)
655	658	TURN		might get lost (downstream of altered splice site)
662	671	HELIX		might get lost (downstream of altered splice site)
671	671	MOD_RES	Omega-N-methylarginine; by PRMT5.	might get lost (downstream of altered splice site)
671	671	MUTAGEN	R->K: Increased kinase activity and stability in response to EGF treatment.	might get lost (downstream of altered splice site)
678	680	HELIX		might get lost (downstream of altered splice site)
687	696	HELIX		might get lost (downstream of altered splice site)
701	703	HELIX		might get lost (downstream of altered splice site)
707	719	HELIX		might get lost (downstream of altered splice site)
729	729	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
750	750	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
753	753	MOD_RES	Phosphothreonine; by MAPK1.	might get lost (downstream of altered splice site)
766	766	CONFLICT	H -> 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

strand

-1

last intron/exon boundary

2189

theoretical NMD boundary in CDS

2077

length of CDS

2301

coding sequence (CDS) position

1741

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

1802

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

170578

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

140453987

original gDNA sequence snippet

ACAGAGACCTCAAGAGTAATAGTATCCTTCCTGAAATTTGT

altered gDNA sequence snippet

ACAGAGACCTCAAGAGTAATGGTATCCTTCCTGAAATTTGT

original cDNA sequence snippet

ACAGAGACCTCAAGAGTAATAATATATTTCTTCATGAAGAC

altered cDNA sequence snippet

ACAGAGACCTCAAGAGTAATGATATATTTCTTCATGAAGAC

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 DIFLHEDLTV KIGDFGLATV
KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM TGQLPYSNIN
NRDQIIFMVG RGYLSPDLSK VRSNCPKAMK RLMAECLKKK RDERPLFPQI LASIELLARS
LPKIHRSASE PSLNRAGFQT EDFSLYACAS PKTPIQAGGY GAFPVH*

speed

0.65 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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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems