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: ENST00000377705
MT speed 0 s - this script 2.973788 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NOL9	polymorphism_automatic	2.0264257050151e-08	simple_aae				R10W	single base exchange	rs4908923		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999979735743 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:6614535G>AN/A show variant in all transcripts IGV

HGNC symbol

NOL9

Ensembl transcript ID

ENST00000377705

Genbank transcript ID

NM_024654

UniProt peptide

Q5SY16

alteration type

single base exchange

alteration region

CDS

DNA changes

c.28C>T
cDNA.61C>T
g.61C>T

AA changes

R10W Score: 101 explain score(s)

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

frameshift

known variant

Reference ID: rs4908923

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1387	843	2230
ExAC	-	-	-

regulatory features

ZBTB33, Transcription Factor, ZBTB33 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
Cjun, Transcription Factor, Cjun TF binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
CBP, Transcription Factor, CBP Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCFL, Transcription Factor, CTCFL Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
Pax5, Transcription Factor, Pax5 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.694	0.105
	0.61	0.088
(flanking)	0.67	0.06

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
Donor marginally increased	54	wt: 0.9765 / mu: 0.9796 (marginal change - not scored)	wt: CTGCTGCTAAAGCGG mu: CTGCTGCTAAAGTGG	GCTG\|ctaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000000089

Mmulatta

all identical

ENSMMUG00000023681

Fcatus

no alignment

ENSFCAG00000000658

n/a

Mmusculus

all identical

ENSMUSG00000028948

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077751

n/a

Dmelanogaster

no alignment

FBgn0034073

n/a

Celegans

no alignment

K09B11.2

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2109 / 2109

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

703 / 703

position of stopcodon in wt / mu cDNA

2142 / 2142

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

34 / 34

chromosome

strand

-1

last intron/exon boundary

1993

theoretical NMD boundary in CDS

1909

length of CDS

2109

coding sequence (CDS) position

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

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

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

6614535

original gDNA sequence snippet

ACTCGGGACTGCTGCTAAAGCGGGGTTCCTGCCGTTCCACT

altered gDNA sequence snippet

ACTCGGGACTGCTGCTAAAGTGGGGTTCCTGCCGTTCCACT

original cDNA sequence snippet

ACTCGGGACTGCTGCTAAAGCGGGGTTCCTGCCGTTCCACT

altered cDNA sequence snippet

ACTCGGGACTGCTGCTAAAGTGGGGTTCCTGCCGTTCCACT

wildtype AA sequence

MADSGLLLKR GSCRSTWLRV RKARPQLILS RRPRRRLGSL RWCGRRRLRW RLLQAQASGV
DWREGARQVS RAAAARRPNT ATPSPIPSPT PASEPESEPE LESASSCHRP LLIPPVRPVG
PGRALLLLPV EQGFTFSGIC RVTCLYGQVQ VFGFTISQGQ PAQDIFSVYT HSCLSIHALH
YSQPEKSKKE LKREARNLLK SHLNLDDRRW SMQNFSPQCS IVLLEHLKTA TVNFITSYPG
SSYIFVQESP TPQIKPEYLA LRSVGIRREK KRKGLQLTES TLSALEELVN VSCEEVDGCP
VILVCGSQDV GKSTFNRYLI NHLLNSLPCV DYLECDLGQT EFTPPGCISL LNITEPVLGP
PFTHLRTPQK MVYYGKPSCK NNYENYIDIV KYVFSAYKRE SPLIVNTMGW VSDQGLLLLI
DLIRLLSPSH VVQFRSDHSK YMPDLTPQYV DDMDGLYTKS KTKMRNRRFR LAAFADALEF
ADEEKESPVE FTGHKLIGVY TDFAFRITPR NRESHNKILR DLSILSYLSQ LQPPMPKPLS
PLHSLTPYQV PFNAVALRIT HSDVAPTHIL YAVNASWVGL CKIQDDVRGY TNGPILLAQT
PICDCLGFGI CRGIDMEKRL YHILTPVPPE ELRTVNCLLV GAIAIPHCVL KCQRGIEGTV
PYVTTDYNFK LPGASEKIGA REPEEAHKEK PYRRPKFCRK MK*

mutated AA sequence

MADSGLLLKW GSCRSTWLRV RKARPQLILS RRPRRRLGSL RWCGRRRLRW RLLQAQASGV
DWREGARQVS RAAAARRPNT ATPSPIPSPT PASEPESEPE LESASSCHRP LLIPPVRPVG
PGRALLLLPV EQGFTFSGIC RVTCLYGQVQ VFGFTISQGQ PAQDIFSVYT HSCLSIHALH
YSQPEKSKKE LKREARNLLK SHLNLDDRRW SMQNFSPQCS IVLLEHLKTA TVNFITSYPG
SSYIFVQESP TPQIKPEYLA LRSVGIRREK KRKGLQLTES TLSALEELVN VSCEEVDGCP
VILVCGSQDV GKSTFNRYLI NHLLNSLPCV DYLECDLGQT EFTPPGCISL LNITEPVLGP
PFTHLRTPQK MVYYGKPSCK NNYENYIDIV KYVFSAYKRE SPLIVNTMGW VSDQGLLLLI
DLIRLLSPSH VVQFRSDHSK YMPDLTPQYV DDMDGLYTKS KTKMRNRRFR LAAFADALEF
ADEEKESPVE FTGHKLIGVY TDFAFRITPR NRESHNKILR DLSILSYLSQ LQPPMPKPLS
PLHSLTPYQV PFNAVALRIT HSDVAPTHIL YAVNASWVGL CKIQDDVRGY TNGPILLAQT
PICDCLGFGI CRGIDMEKRL YHILTPVPPE ELRTVNCLLV GAIAIPHCVL KCQRGIEGTV
PYVTTDYNFK LPGASEKIGA REPEEAHKEK PYRRPKFCRK MK*

speed

0.97 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