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: ENST00000328570
MT speed 0 s - this script 3.120037 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR2T29	polymorphism_automatic	1.26199051209142e-12	simple_aae				F154S	single base exchange	rs533808122		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998738 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:248722332A>GN/A show variant in all transcripts IGV

HGNC symbol

OR2T29

Ensembl transcript ID

ENST00000328570

Genbank transcript ID

NM_001004694

UniProt peptide

Q8NH02

alteration type

single base exchange

alteration region

CDS

DNA changes

c.461T>C
cDNA.466T>C
g.466T>C

AA changes

F154S Score: 155 explain score(s)

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

154

frameshift

known variant

Reference ID: rs533808122

database	homozygous (G/G)	heterozygous	allele carriers
1000G	106	1504	1610
ExAC	5	26	31

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.049	0.001
	0.263	0.003
(flanking)	-0.105	0.007

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

466

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

154

mutated

not conserved

154

Ptroglodytes

all identical

ENSPTRG00000002221

154

Mmulatta

not conserved

ENSMMUG00000030576

154

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000050818

154

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
144	162	TRANSMEM	Helical; Name=4; (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

948 / 948

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

316 / 316

position of stopcodon in wt / mu cDNA

953 / 953

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

6 / 6

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

948

coding sequence (CDS) position

461

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

466

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

466

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

248722332

original gDNA sequence snippet

CCTGGCATCGGGCTGCTGGTTCCTGGGCTCAGTGGATGGCT

altered gDNA sequence snippet

CCTGGCATCGGGCTGCTGGTCCCTGGGCTCAGTGGATGGCT

original cDNA sequence snippet

CCTGGCATCGGGCTGCTGGTTCCTGGGCTCAGTGGATGGCT

altered cDNA sequence snippet

CCTGGCATCGGGCTGCTGGTCCCTGGGCTCAGTGGATGGCT

wildtype AA sequence

MANITRMANH TGRLDFILMG LFRQSKHPAL LSVVIFVVFL KALSGNAVLI LLIHCDAHLH
SPMYFFISQL SLMDMAYISV TVPKMLLDQV MGVNKVSAPE CGMQMFLYLT LAGSEFFLLA
TMAYDRYVAI CHPLRYPVLM NHRVCLFLAS GCWFLGSVDG FMLTPITMSF PFCRSWEIHH
FFCEVPAVTI LSCSDTSLYE TLMYLCCVLM LLIPVTIISS SYLLILLTVH RMNSAEGRKK
AFATCSSHLT VVILFYGAAV YTYMLPSSYH TPEKDMMVSV FYTILTPVLN PLIYSLRNKD
VMGALKKMLT VRFVL*

mutated AA sequence

MANITRMANH TGRLDFILMG LFRQSKHPAL LSVVIFVVFL KALSGNAVLI LLIHCDAHLH
SPMYFFISQL SLMDMAYISV TVPKMLLDQV MGVNKVSAPE CGMQMFLYLT LAGSEFFLLA
TMAYDRYVAI CHPLRYPVLM NHRVCLFLAS GCWSLGSVDG FMLTPITMSF PFCRSWEIHH
FFCEVPAVTI LSCSDTSLYE TLMYLCCVLM LLIPVTIISS SYLLILLTVH RMNSAEGRKK
AFATCSSHLT VVILFYGAAV YTYMLPSSYH TPEKDMMVSV FYTILTPVLN PLIYSLRNKD
VMGALKKMLT VRFVL*

speed

1.09 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