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: ENST00000300127
MT speed 1.33 s - this script 3.430604 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR4D6	polymorphism_automatic	1.2250200853714e-12	simple_aae		affected		S151T	single base exchange	rs1453542		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998775 (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)

chr11:59224885G>CN/A show variant in all transcripts IGV

HGNC symbol

OR4D6

Ensembl transcript ID

ENST00000300127

Genbank transcript ID

NM_001004708

UniProt peptide

Q8NGJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.452G>C
cDNA.475G>C
g.475G>C

AA changes

S151T Score: 58 explain score(s)

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

151

frameshift

known variant

Reference ID: rs1453542

database	homozygous (C/C)	heterozygous	allele carriers
1000G	98	692	790
ExAC	4433	22123	26556

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.947	0.024
	0.835	0.018
(flanking)	-1.132	0.008

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 marginally increased	470	wt: 0.8367 / mu: 0.8758 (marginal change - not scored)	wt: GCCTTGGTGGTGGCTTCTTGGGTGAGTGGTGGTTTGCATTC mu: GCCTTGGTGGTGGCTTCTTGGGTGACTGGTGGTTTGCATTC	ttgg\|GTGA
Acc gained	477	0.54	mu: TGGTGGCTTCTTGGGTGACTGGTGGTTTGCATTCAATCATC	actg\|GTGG

distance from splice site

475

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

151

mutated

all conserved

151

Ptroglodytes

all identical

ENSPTRG00000003692

151

Mmulatta

not conserved

ENSMMUG00000014114

151

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000067524

151

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
140	158	TRANSMEM	Helical; Name=4; (Potential).	lost
159	195	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
189	189	DISULFID	By similarity.	might get lost (downstream of altered splice site)
196	219	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
220	235	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
236	258	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
259	269	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
270	289	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
290	314	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

945 / 945

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

315 / 315

position of stopcodon in wt / mu cDNA

968 / 968

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

24 / 24

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

945

coding sequence (CDS) position

452

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

475

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

475

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

59224885

original gDNA sequence snippet

GGTGGTGGCTTCTTGGGTGAGTGGTGGTTTGCATTCAATCA

altered gDNA sequence snippet

GGTGGTGGCTTCTTGGGTGACTGGTGGTTTGCATTCAATCA

original cDNA sequence snippet

GGTGGTGGCTTCTTGGGTGAGTGGTGGTTTGCATTCAATCA

altered cDNA sequence snippet

GGTGGTGGCTTCTTGGGTGACTGGTGGTTTGCATTCAATCA

wildtype AA sequence

MDQINHTNVK EFFFLELTRS RELEFFLFVV FFAVYVATVL GNALIVVTIT CESRLHTPMY
FLLRNKSVLD IVFSSITVPK FLVDLLSDRK TISYNDCMAQ IFFFHFAGGA DIFFLSVMAY
DRYLAIAKPL HYVTMMRKEV WVALVVASWV SGGLHSIIQV ILMLPFPFCG PNTLDAFYCY
VLQVVKLACT DTFALELFMI SNNGLVTLLW FLLLLGSYTV ILVMLRSHSG EGRNKALSTC
TSHMLVVTLH FVPCVYIYCR PFMTLPMDTT ISINNTVITP MLNPIIYSLR NQEMKSAMQR
LQRRLGPSES RKWG*

mutated AA sequence

MDQINHTNVK EFFFLELTRS RELEFFLFVV FFAVYVATVL GNALIVVTIT CESRLHTPMY
FLLRNKSVLD IVFSSITVPK FLVDLLSDRK TISYNDCMAQ IFFFHFAGGA DIFFLSVMAY
DRYLAIAKPL HYVTMMRKEV WVALVVASWV TGGLHSIIQV ILMLPFPFCG PNTLDAFYCY
VLQVVKLACT DTFALELFMI SNNGLVTLLW FLLLLGSYTV ILVMLRSHSG EGRNKALSTC
TSHMLVVTLH FVPCVYIYCR PFMTLPMDTT ISINNTVITP MLNPIIYSLR NQEMKSAMQR
LQRRLGPSES RKWG*

speed

1.33 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