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: ENST00000408898
MT speed 0 s - this script 3.029224 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR2A25	polymorphism_automatic	4.17223300352987e-09	simple_aae		affected		A209P	single base exchange	rs2961135		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999995827767 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM141875)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:143771937G>CN/A show variant in all transcripts IGV

HGNC symbol

OR2A25

Ensembl transcript ID

ENST00000408898

Genbank transcript ID

NM_001004488

UniProt peptide

A4D2G3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.625G>C
cDNA.663G>C
g.663G>C

AA changes

A209P Score: 27 explain score(s)

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

209

frameshift

known variant

Reference ID: rs2961135

database	homozygous (C/C)	heterozygous	allele carriers
1000G	977	1117	2094
ExAC	19978	-7189	12789

known disease mutation at this position, please check HGMD for details (HGMD ID CM141875)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.422	0.006
	1.303	0.27
(flanking)	3.609	0.315

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 increased	674	wt: 0.66 / mu: 0.85	wt: CTGGTGGGAGCCTTCTTTTCCACTGTAATATCTTATGTTCA mu: CTGGTGGGACCCTTCTTTTCCACTGTAATATCTTATGTTCA	ttcc\|ACTG

distance from splice site

352

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

not conserved

209

Ptroglodytes

not conserved

ENSPTRG00000040462

209

Mmulatta

not conserved

ENSMMUG00000013318

209

Fcatus

not conserved

ENSFCAG00000018106

209

Mmusculus

not conserved

ENSMUSG00000045708

209

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
196	218	TRANSMEM	Helical; Name=5; (Potential).	lost
219	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	271	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
272	291	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
292	310	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

933 / 933

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

311 / 311

position of stopcodon in wt / mu cDNA

971 / 971

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

39 / 39

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

933

coding sequence (CDS) position

625

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

663

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

663

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

143771937

original gDNA sequence snippet

CAGTGTCTGTGCTGGTGGGAGCCTTCTTTTCCACTGTAATA

altered gDNA sequence snippet

CAGTGTCTGTGCTGGTGGGACCCTTCTTTTCCACTGTAATA

original cDNA sequence snippet

CAGTGTCTGTGCTGGTGGGAGCCTTCTTTTCCACTGTAATA

altered cDNA sequence snippet

CAGTGTCTGTGCTGGTGGGACCCTTCTTTTCCACTGTAATA

wildtype AA sequence

MGGNQTSITE FLLLGFPIGP RIQMLLFGLF SLFYIFILLG NGTILGLISL DSRLHTPMYF
FLSHLAVVDI ACACSTVPQM LVNLLHPAKP ISFAGCMTQM FLFLSFAHTE CLLLVVMSYD
RYVAICHPLR YSTIMTWKVC ITLALTSWIL GVLLALVHLV LLLPLSFCGP QKLNHFFCEI
MAVLKLACAD THINEVMVLA GAVSVLVGAF FSTVISYVHI LCAILKIQSG EGCQKAFSIC
SSHLCVVGLF YGTAIIMYVE PQYESPKEQK KYLLLFHSLF NPMLNPLIYS LRNKEVQGTL
KRMLEKKRTS *

mutated AA sequence

MGGNQTSITE FLLLGFPIGP RIQMLLFGLF SLFYIFILLG NGTILGLISL DSRLHTPMYF
FLSHLAVVDI ACACSTVPQM LVNLLHPAKP ISFAGCMTQM FLFLSFAHTE CLLLVVMSYD
RYVAICHPLR YSTIMTWKVC ITLALTSWIL GVLLALVHLV LLLPLSFCGP QKLNHFFCEI
MAVLKLACAD THINEVMVLA GAVSVLVGPF FSTVISYVHI LCAILKIQSG EGCQKAFSIC
SSHLCVVGLF YGTAIIMYVE PQYESPKEQK KYLLLFHSLF NPMLNPLIYS LRNKEVQGTL
KRMLEKKRTS *

speed

0.96 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