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: ENST00000319968
MT speed 0 s - this script 2.725216 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR2T8	polymorphism_automatic	3.71302988355637e-12	simple_aae		affected		A169V	single base exchange	rs61857492		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999996287 (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)

chr1:248084825C>TN/A show variant in all transcripts IGV

HGNC symbol

OR2T8

Ensembl transcript ID

ENST00000319968

Genbank transcript ID

NM_001005522

UniProt peptide

A6NH00

alteration type

single base exchange

alteration region

CDS

DNA changes

c.506C>T
cDNA.506C>T
g.506C>T

AA changes

A169V Score: 64 explain score(s)

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

169

frameshift

known variant

Reference ID: rs61857492

database	homozygous (T/T)	heterozygous	allele carriers
1000G	59	2266	2325
ExAC	651	31465	32116

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.075	0
	0.45	0
(flanking)	-1.263	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
Acc marginally increased	496	wt: 0.7876 / mu: 0.8038 (marginal change - not scored)	wt: TTGCTACCCTGAGCTTCCCATATTGCGGTGCACACGAGATC mu: TTGCTACCCTGAGCTTCCCATATTGCGGTGTACACGAGATC	ccat\|ATTG
Donor increased	499	wt: 0.88 / mu: 0.97	wt: CATATTGCGGTGCAC mu: CATATTGCGGTGTAC	TATT\|gcgg

distance from splice site

434

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

169

mutated

not conserved

169

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000018892

169

Fcatus

all identical

ENSFCAG00000004483

169

Mmusculus

not conserved

ENSMUSG00000059504

169

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
165	201	TOPO_DOM	Extracellular (Potential).	lost
177	177	DISULFID	By similarity.	might get lost (downstream of altered splice site)
202	222	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
223	234	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
256	269	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
270	290	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
291	312	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

939 / 939

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

313 / 313

position of stopcodon in wt / mu cDNA

939 / 939

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

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

939

coding sequence (CDS) position

506

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

506

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

506

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

248084825

original gDNA sequence snippet

GAGCTTCCCATATTGCGGTGCACACGAGATCGATCACTTCT

altered gDNA sequence snippet

GAGCTTCCCATATTGCGGTGTACACGAGATCGATCACTTCT

original cDNA sequence snippet

GAGCTTCCCATATTGCGGTGCACACGAGATCGATCACTTCT

altered cDNA sequence snippet

GAGCTTCCCATATTGCGGTGTACACGAGATCGATCACTTCT

wildtype AA sequence

MENGSYTSYF ILLGLFNHTR AHQVLFMMVL SIVLTSLFGN SLMILLIHWD HRLHTPMYFL
LSQLSLMDVM LVSTTVPKMA ADYLTGSKAI SRAGCGAQIF FLPTLGGGEC FLLAAMAYDR
YAAVCHPLRY PTLMSWQLCL RMNLSCWLLG AADGLLQAVA TLSFPYCGAH EIDHFFCETP
VLVRLACADT SVFENAMYIC CVLMLLVPFS LILSSYGLIL AAVLHMRSTE ARKKAFATCS
SHVAVVGLFY GAAIFTYMRP KSHRSTNHDK VVSAFYTMFT PLLNPLIYSV KNSEVKGALT
RCMGRCVALS RE*

mutated AA sequence

MENGSYTSYF ILLGLFNHTR AHQVLFMMVL SIVLTSLFGN SLMILLIHWD HRLHTPMYFL
LSQLSLMDVM LVSTTVPKMA ADYLTGSKAI SRAGCGAQIF FLPTLGGGEC FLLAAMAYDR
YAAVCHPLRY PTLMSWQLCL RMNLSCWLLG AADGLLQAVA TLSFPYCGVH EIDHFFCETP
VLVRLACADT SVFENAMYIC CVLMLLVPFS LILSSYGLIL AAVLHMRSTE ARKKAFATCS
SHVAVVGLFY GAAIFTYMRP KSHRSTNHDK VVSAFYTMFT PLLNPLIYSV KNSEVKGALT
RCMGRCVALS RE*

speed

0.70 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