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: ENST00000159060
MT speed 0 s - this script 3.01665 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
NOX3	polymorphism_automatic	0.990329051487992	simple_aae		affected		T171K	single base exchange	rs3749930		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00967094851200792 (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)

chr6:155761246G>TN/A show variant in all transcripts IGV

HGNC symbol

NOX3

Ensembl transcript ID

ENST00000159060

Genbank transcript ID

NM_015718

UniProt peptide

Q9HBY0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.512C>A
cDNA.615C>A
g.15792C>A

AA changes

T171K Score: 78 explain score(s)

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

171

frameshift

known variant

Reference ID: rs3749930

database	homozygous (T/T)	heterozygous	allele carriers
1000G	153	683	836
ExAC	2038	11314	13352

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.167	0.215
	4.068	0.666
(flanking)	1.427	0.598

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 increased	15788	wt: 0.26 / mu: 1.00	wt: TGCTAAGGACAATAG mu: TGCTAAGGAAAATAG	CTAA\|ggac
Donor marginally increased	15789	wt: 0.9789 / mu: 0.9817 (marginal change - not scored)	wt: GCTAAGGACAATAGC mu: GCTAAGGAAAATAGC	TAAG\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

171

mutated

not conserved

171

Ptroglodytes

all identical

ENSPTRG00000018732

171

Mmulatta

all identical

ENSMMUG00000008762

171

Fcatus

all identical

ENSFCAG00000006165

171

Mmusculus

all identical

ENSMUSG00000023802

191

Ggallus

all identical

ENSGALG00000013659

171

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
55	284	DOMAIN	Ferric oxidoreductase.	lost
168	188	TRANSMEM	Helical; (Potential).	lost
189	201	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
202	222	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
223	395	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
238	238	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
285	395	DOMAIN	FAD-binding FR-type.	might get lost (downstream of altered splice site)
328	328	CONFLICT	P -> S (in Ref. 3; AAG15435).	might get lost (downstream of altered splice site)
396	416	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
413	413	MUTAGEN	P->H: Loss of catalytic activity.	might get lost (downstream of altered splice site)
417	568	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1707 / 1707

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

569 / 569

position of stopcodon in wt / mu cDNA

1810 / 1810

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

104 / 104

chromosome

strand

-1

last intron/exon boundary

1838

theoretical NMD boundary in CDS

1684

length of CDS

1707

coding sequence (CDS) position

512

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

615

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

15792

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

155761246

original gDNA sequence snippet

AACCACTGAATTGCTAAGGACAATAGCAGGCGTCACCGGTC

altered gDNA sequence snippet

AACCACTGAATTGCTAAGGAAAATAGCAGGCGTCACCGGTC

original cDNA sequence snippet

AACCACTGAATTGCTAAGGACAATAGCAGGCGTCACCGGTC

altered cDNA sequence snippet

AACCACTGAATTGCTAAGGAAAATAGCAGGCGTCACCGGTC

wildtype AA sequence

MMGCWILNEG LSTILVLSWL GINFYLFIDT FYWYEEEESF HYTRVILGST LAWARASALC
LNFNCMLILI PVSRNLISFI RGTSICCRGP WRRQLDKNLR FHKLVAYGIA VNATIHIVAH
FFNLERYHWS QSEEAQGLLA ALSKLGNTPN ESYLNPVRTF PTNTTTELLR TIAGVTGLVI
SLALVLIMTS STEFIRQASY ELFWYTHHVF IVFFLSLAIH GTGRIVRGQT QDSLSLHNIT
FCRDRYAEWQ TVAQCPVPQF SGKEPSAWKW ILGPVVLYAC ERIIRFWRFQ QEVVITKVVS
HPSGVLELHM KKRGFKMAPG QYILVQCPAI SSLEWHPFTL TSAPQEDFFS VHIRAAGDWT
AALLEAFGAE GQALQEPWSL PRLAVDGPFG TALTDVFHYP VCVCVAAGIG VTPFAALLKS
IWYKCSEAQT PLKLSKVYFY WICRDARAFE WFADLLLSLE TRMSEQGKTH FLSYHIFLTG
WDENQALHIA LHWDENTDVI TGLKQKTFYG RPNWNNEFKQ IAYNHPSSSI GVFFCGPKAL
SRTLQKMCHL YSSADPRGVH FYYNKESF*

mutated AA sequence

MMGCWILNEG LSTILVLSWL GINFYLFIDT FYWYEEEESF HYTRVILGST LAWARASALC
LNFNCMLILI PVSRNLISFI RGTSICCRGP WRRQLDKNLR FHKLVAYGIA VNATIHIVAH
FFNLERYHWS QSEEAQGLLA ALSKLGNTPN ESYLNPVRTF PTNTTTELLR KIAGVTGLVI
SLALVLIMTS STEFIRQASY ELFWYTHHVF IVFFLSLAIH GTGRIVRGQT QDSLSLHNIT
FCRDRYAEWQ TVAQCPVPQF SGKEPSAWKW ILGPVVLYAC ERIIRFWRFQ QEVVITKVVS
HPSGVLELHM KKRGFKMAPG QYILVQCPAI SSLEWHPFTL TSAPQEDFFS VHIRAAGDWT
AALLEAFGAE GQALQEPWSL PRLAVDGPFG TALTDVFHYP VCVCVAAGIG VTPFAALLKS
IWYKCSEAQT PLKLSKVYFY WICRDARAFE WFADLLLSLE TRMSEQGKTH FLSYHIFLTG
WDENQALHIA LHWDENTDVI TGLKQKTFYG RPNWNNEFKQ IAYNHPSSSI GVFFCGPKAL
SRTLQKMCHL YSSADPRGVH FYYNKESF*

speed

0.95 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