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: ENST00000304880
MT speed 0 s - this script 2.192011 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR1N1	polymorphism_automatic	1.49880108324396e-14	simple_aae		affected		P18S	single base exchange	rs10818708		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999985 (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)

chr9:125289521G>AN/A show variant in all transcripts IGV

HGNC symbol

OR1N1

Ensembl transcript ID

ENST00000304880

Genbank transcript ID

NM_012363

UniProt peptide

Q8NGS0

alteration type

single base exchange

alteration region

CDS

DNA changes

c.52C>T
cDNA.52C>T
g.52C>T

AA changes

P18S Score: 74 explain score(s)

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

frameshift

known variant

Reference ID: rs10818708

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1311	926	2237
ExAC	20735	-8703	12032

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.585	0
	-0.633	0
(flanking)	-1.864	0

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 gained	45	0.78	mu: GGAATATCAGCGTCT	AATA\|tcag

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

not conserved

ENSPTRG00000021328

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000075383

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1	23	TOPO_DOM	Extracellular (Potential).	lost
24	47	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
48	55	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
56	77	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
78	98	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
91	91	CONFLICT	S -> T (in Ref. 4; AAC39612).	might get lost (downstream of altered splice site)
95	95	DISULFID	By similarity.	might get lost (downstream of altered splice site)
99	118	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
119	137	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
138	156	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
157	194	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
187	187	DISULFID	By similarity.	might get lost (downstream of altered splice site)
195	217	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
218	234	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
235	257	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
258	270	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
271	290	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
291	311	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

936 / 936

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

312 / 312

position of stopcodon in wt / mu cDNA

936 / 936

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

936

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)

125289521

original gDNA sequence snippet

TCCTCCGAGGAATATCAGCGCCTCCAGAGCAACAGCAGTCC

altered gDNA sequence snippet

TCCTCCGAGGAATATCAGCGTCTCCAGAGCAACAGCAGTCC

original cDNA sequence snippet

TCCTCCGAGGAATATCAGCGCCTCCAGAGCAACAGCAGTCC

altered cDNA sequence snippet

TCCTCCGAGGAATATCAGCGTCTCCAGAGCAACAGCAGTCC

wildtype AA sequence

MENQSSISEF FLRGISAPPE QQQSLFGIFL CMYLVTLTGN LLIILAIGSD LHLHTPMYFF
LANLSFVDMG LTSSTVTKML VNIQTRHHTI SYTGCLTQMY FFLMFGDLDS FFLAAMAYDR
YVAICHPLCY STVMRPQVCA LMLALCWVLT NIVALTHTFL MARLSFCVTG EIAHFFCDIT
PVLKLSCSDT HINEMMVFVL GGTVLIVPFL CIVTSYIHIV PAILRVRTRG GVGKAFSTCS
SHLCVVCVFY GTLFSAYLCP PSIASEEKDI AAAAMYTIVT PMLNPFIYSL RNKDMKGALK
RLFSHRSIVS S*

mutated AA sequence

MENQSSISEF FLRGISASPE QQQSLFGIFL CMYLVTLTGN LLIILAIGSD LHLHTPMYFF
LANLSFVDMG LTSSTVTKML VNIQTRHHTI SYTGCLTQMY FFLMFGDLDS FFLAAMAYDR
YVAICHPLCY STVMRPQVCA LMLALCWVLT NIVALTHTFL MARLSFCVTG EIAHFFCDIT
PVLKLSCSDT HINEMMVFVL GGTVLIVPFL CIVTSYIHIV PAILRVRTRG GVGKAFSTCS
SHLCVVCVFY GTLFSAYLCP PSIASEEKDI AAAAMYTIVT PMLNPFIYSL RNKDMKGALK
RLFSHRSIVS S*

speed

0.13 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