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: ENST00000423932
MT speed 0 s - this script 3.360162 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR10J1	polymorphism_automatic	6.42399466954657e-11	simple_aae		affected		I103M	single base exchange	rs12048482		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99999999993576 (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)

chr1:159409857A>GN/A show variant in all transcripts IGV

HGNC symbol

OR10J1

Ensembl transcript ID

ENST00000423932

Genbank transcript ID

NM_012351

UniProt peptide

P30954

alteration type

single base exchange

alteration region

CDS

DNA changes

c.309A>G
cDNA.346A>G
g.346A>G

AA changes

I103M Score: 10 explain score(s)

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

103

frameshift

known variant

Reference ID: rs12048482

database	homozygous (G/G)	heterozygous	allele carriers
1000G	625	1152	1777
ExAC	20227	-7687	12540

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.074	0.002
	0.11	0
(flanking)	-0.293	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	340	0.78	mu: AGCCAGCCCATGTCA	CCAG\|ccca

distance from splice site

346

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

103

mutated

all conserved

103

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000001823

102

Mmusculus

all identical

ENSMUSG00000049605

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
87	110	TOPO_DOM	Extracellular (Potential).	lost
108	108	DISULFID	By similarity.	might get lost (downstream of altered splice site)
111	131	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
132	150	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
151	171	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
172	207	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
199	199	DISULFID	By similarity.	might get lost (downstream of altered splice site)
208	227	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
228	247	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
248	268	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
269	281	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
282	302	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
303	320	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

963 / 963

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

321 / 321

position of stopcodon in wt / mu cDNA

1000 / 1000

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

38 / 38

chromosome

strand

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

963

coding sequence (CDS) position

309

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

346

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

346

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

159409857

original gDNA sequence snippet

GTAGGTATGAGCCAGCCCATATCATTGGCAGGGTGTGCCAC

altered gDNA sequence snippet

GTAGGTATGAGCCAGCCCATGTCATTGGCAGGGTGTGCCAC

original cDNA sequence snippet

GTAGGTATGAGCCAGCCCATATCATTGGCAGGGTGTGCCAC

altered cDNA sequence snippet

GTAGGTATGAGCCAGCCCATGTCATTGGCAGGGTGTGCCAC

wildtype AA sequence

MLLCFRFGNQ SMKRENFTLI TDFVFQGFSS FHEQQITLFG VFLALYILTL AGNIIIVTII
RMDLHLHTPM YFFLSMLSTS ETVYTLVILP RMLSSLVGMS QPISLAGCAT QMFFFVTFGI
TNCFLLTAMG YDRYVAICNP LRYMVIMNKR LRIQLVLGAC SIGLIVAITQ VTSVFRLPFC
ARKVPHFFCD IRPVMKLSCI DTTVNEILTL IISVLVLVVP MGLVFISYVL IISTILKIAS
VEGRKKAFAT CASHLTVVIV HYSCASIAYL KPKSENTREH DQLISVTYTV ITPLLNPVVY
TLRNKEVKDA LCRAVGGKFS *

mutated AA sequence

MLLCFRFGNQ SMKRENFTLI TDFVFQGFSS FHEQQITLFG VFLALYILTL AGNIIIVTII
RMDLHLHTPM YFFLSMLSTS ETVYTLVILP RMLSSLVGMS QPMSLAGCAT QMFFFVTFGI
TNCFLLTAMG YDRYVAICNP LRYMVIMNKR LRIQLVLGAC SIGLIVAITQ VTSVFRLPFC
ARKVPHFFCD IRPVMKLSCI DTTVNEILTL IISVLVLVVP MGLVFISYVL IISTILKIAS
VEGRKKAFAT CASHLTVVIV HYSCASIAYL KPKSENTREH DQLISVTYTV ITPLLNPVVY
TLRNKEVKDA LCRAVGGKFS *

speed

1.28 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