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: ENST00000367996
MT speed 0 s - this script 3.065846 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ADAMTS4	polymorphism_automatic	9.81860204252172e-09	simple_aae		affected		Q626R	single base exchange	rs4233367		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999990181398 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:161163037T>CN/A show variant in all transcripts IGV

HGNC symbol

ADAMTS4

Ensembl transcript ID

ENST00000367996

Genbank transcript ID

NM_005099

UniProt peptide

O75173

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1877A>G
cDNA.2306A>G
g.5810A>G

AA changes

Q626R Score: 43 explain score(s)

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

626

frameshift

known variant

Reference ID: rs4233367

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1285	970	2255
ExAC	26837	-20907	5930

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.6	0.999
	0.509	0.998
(flanking)	1.609	1

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

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	5804	wt: 0.23 / mu: 0.28	wt: CCAGTGCAAACTCACCTGCCAGGCCCAGGCACTGGGCTACT mu: CCAGTGCAAACTCACCTGCCAGGCCCGGGCACTGGGCTACT	gcca\|GGCC
Donor gained	5804	0.66	mu: CTGCCAGGCCCGGGC	GCCA\|ggcc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

626

mutated

all conserved

626

Ptroglodytes

all conserved

ENSPTRG00000001576

626

Mmulatta

all conserved

ENSMMUG00000018132

626

Fcatus

all conserved

ENSFCAG00000000494

622

Mmusculus

all conserved

ENSMUSG00000006403

634

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

not conserved

F25H8.3

708

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
577	685	COMPBIAS	Cys-rich.	lost
682	682	CONFLICT	G -> R (in Ref. 2; AAL02262).	might get lost (downstream of altered splice site)
686	837	REGION	Spacer.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2514 / 2514

position (AA) of stopcodon in wt / mu AA sequence

838 / 838

position of stopcodon in wt / mu cDNA

2943 / 2943

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

430 / 430

chromosome

strand

-1

last intron/exon boundary

2517

theoretical NMD boundary in CDS

2037

length of CDS

2514

coding sequence (CDS) position

1877

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

2306

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

5810

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

161163037

original gDNA sequence snippet

CAAACTCACCTGCCAGGCCCAGGCACTGGGCTACTACTATG

altered gDNA sequence snippet

CAAACTCACCTGCCAGGCCCGGGCACTGGGCTACTACTATG

original cDNA sequence snippet

CAAACTCACCTGCCAGGCCCAGGCACTGGGCTACTACTATG

altered cDNA sequence snippet

CAAACTCACCTGCCAGGCCCGGGCACTGGGCTACTACTATG

wildtype AA sequence

MSQTGSHPGR GLAGRWLWGA QPCLLLPIVP LSWLVWLLLL LLASLLPSAR LASPLPREEE
IVFPEKLNGS VLPGSGAPAR LLCRLQAFGE TLLLELEQDS GVQVEGLTVQ YLGQAPELLG
GAEPGTYLTG TINGDPESVA SLHWDGGALL GVLQYRGAEL HLQPLEGGTP NSAGGPGAHI
LRRKSPASGQ GPMCNVKAPL GSPSPRPRRA KRFASLSRFV ETLVVADDKM AAFHGAGLKR
YLLTVMAAAA KAFKHPSIRN PVSLVVTRLV ILGSGEEGPQ VGPSAAQTLR SFCAWQRGLN
TPEDSDPDHF DTAILFTRQD LCGVSTCDTL GMADVGTVCD PARSCAIVED DGLQSAFTAA
HELGHVFNML HDNSKPCISL NGPLSTSRHV MAPVMAHVDP EEPWSPCSAR FITDFLDNGY
GHCLLDKPEA PLHLPVTFPG KDYDADRQCQ LTFGPDSRHC PQLPPPCAAL WCSGHLNGHA
MCQTKHSPWA DGTPCGPAQA CMGGRCLHMD QLQDFNIPQA GGWGPWGPWG DCSRTCGGGV
QFSSRDCTRP VPRNGGKYCE GRRTRFRSCN TEDCPTGSAL TFREEQCAAY NHRTDLFKSF
PGPMDWVPRY TGVAPQDQCK LTCQAQALGY YYVLEPRVVD GTPCSPDSSS VCVQGRCIHA
GCDRIIGSKK KFDKCMVCGG DGSGCSKQSG SFRKFRYGYN NVVTIPAGAT HILVRQQGNP
GHRSIYLALK LPDGSYALNG EYTLMPSPTD VVLPGAVSLR YSGATAASET LSGHGPLAQP
LTLQVLVAGN PQDTRLRYSF FVPRPTPSTP RPTPQDWLHR RAQILEILRR RPWAGRK*

mutated AA sequence

MSQTGSHPGR GLAGRWLWGA QPCLLLPIVP LSWLVWLLLL LLASLLPSAR LASPLPREEE
IVFPEKLNGS VLPGSGAPAR LLCRLQAFGE TLLLELEQDS GVQVEGLTVQ YLGQAPELLG
GAEPGTYLTG TINGDPESVA SLHWDGGALL GVLQYRGAEL HLQPLEGGTP NSAGGPGAHI
LRRKSPASGQ GPMCNVKAPL GSPSPRPRRA KRFASLSRFV ETLVVADDKM AAFHGAGLKR
YLLTVMAAAA KAFKHPSIRN PVSLVVTRLV ILGSGEEGPQ VGPSAAQTLR SFCAWQRGLN
TPEDSDPDHF DTAILFTRQD LCGVSTCDTL GMADVGTVCD PARSCAIVED DGLQSAFTAA
HELGHVFNML HDNSKPCISL NGPLSTSRHV MAPVMAHVDP EEPWSPCSAR FITDFLDNGY
GHCLLDKPEA PLHLPVTFPG KDYDADRQCQ LTFGPDSRHC PQLPPPCAAL WCSGHLNGHA
MCQTKHSPWA DGTPCGPAQA CMGGRCLHMD QLQDFNIPQA GGWGPWGPWG DCSRTCGGGV
QFSSRDCTRP VPRNGGKYCE GRRTRFRSCN TEDCPTGSAL TFREEQCAAY NHRTDLFKSF
PGPMDWVPRY TGVAPQDQCK LTCQARALGY YYVLEPRVVD GTPCSPDSSS VCVQGRCIHA
GCDRIIGSKK KFDKCMVCGG DGSGCSKQSG SFRKFRYGYN NVVTIPAGAT HILVRQQGNP
GHRSIYLALK LPDGSYALNG EYTLMPSPTD VVLPGAVSLR YSGATAASET LSGHGPLAQP
LTLQVLVAGN PQDTRLRYSF FVPRPTPSTP RPTPQDWLHR RAQILEILRR RPWAGRK*

speed

0.99 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

polymorphism

Problems