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 2.77541 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR2T8	polymorphism_automatic	1.89848137210902e-14	simple_aae		affected		N143T	single base exchange	rs4523549		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999981 (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)

chr1:248084747A>CN/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.428A>C
cDNA.428A>C
g.428A>C

AA changes

N143T Score: 65 explain score(s)

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

143

frameshift

known variant

Reference ID: rs4523549

database	homozygous (C/C)	heterozygous	allele carriers
1000G	2310	102	2412
ExAC	127	13	140

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.426	0
	-0.034	0
(flanking)	-1.969	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 gained	436	0.38	mu: GCCTGAGGATGACCCTGTCGTGTTGGCTCCTGGGTGCAGCT	tcgt\|GTTG

distance from splice site

428

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

143

mutated

not conserved

143

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000018892

143

Fcatus

not conserved

ENSFCAG00000004483

143

Mmusculus

not conserved

ENSMUSG00000059504

143

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
118	143	TOPO_DOM	Cytoplasmic (Potential).	lost
144	164	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
165	201	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
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

428

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

428

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

428

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

248084747

original gDNA sequence snippet

GCAGCTGTGCCTGAGGATGAACCTGTCGTGTTGGCTCCTGG

altered gDNA sequence snippet

GCAGCTGTGCCTGAGGATGACCCTGTCGTGTTGGCTCCTGG

original cDNA sequence snippet

GCAGCTGTGCCTGAGGATGAACCTGTCGTGTTGGCTCCTGG

altered cDNA sequence snippet

GCAGCTGTGCCTGAGGATGACCCTGTCGTGTTGGCTCCTGG

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 RMTLSCWLLG AADGLLQAVA TLSFPYCGAH 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