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: ENST00000366474
MT speed 0 s - this script 2.853732 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR2T1	polymorphism_automatic	9.41025035672283e-13	simple_aae		affected		H25R	single base exchange	rs28599722		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999059 (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)

chr1:248569369A>GN/A show variant in all transcripts IGV

HGNC symbol

OR2T1

Ensembl transcript ID

ENST00000366474

Genbank transcript ID

NM_030904

UniProt peptide

O43869

alteration type

single base exchange

alteration region

CDS

DNA changes

c.74A>G
cDNA.74A>G
g.74A>G

AA changes

H25R Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs28599722

database	homozygous (G/G)	heterozygous	allele carriers
1000G	361	912	1273
ExAC	14224	4319	18543

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.799	0
	0.163	0.001
(flanking)	2.002	0.006

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	82	wt: 0.5525 / mu: 0.6258 (marginal change - not scored)	wt: CAATTAATTCACATGTTGTTATTTTACTGCCCTGGGAATGC mu: CAATTAATTCACGTGTTGTTATTTTACTGCCCTGGGAATGC	gtta\|TTTT
Acc marginally increased	85	wt: 0.8109 / mu: 0.8166 (marginal change - not scored)	wt: TTAATTCACATGTTGTTATTTTACTGCCCTGGGAATGCTAT mu: TTAATTCACGTGTTGTTATTTTACTGCCCTGGGAATGCTAT	attt\|TACT
Donor increased	68	wt: 0.67 / mu: 0.99	wt: AATTAATTCACATGT mu: AATTAATTCACGTGT	TTAA\|ttca
Donor gained	73	0.58	mu: ATTCACGTGTTGTTA	TCAC\|gtgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000030059

Mmulatta

all conserved

ENSMMUG00000031197

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000072707

n/a

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
1	76	TOPO_DOM	Extracellular (Potential).	lost
56	56	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
77	97	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
98	107	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
108	128	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
129	148	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
147	147	DISULFID	By similarity.	might get lost (downstream of altered splice site)
149	169	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
170	191	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
192	212	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
213	247	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
239	239	DISULFID	By similarity.	might get lost (downstream of altered splice site)
248	268	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
269	286	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
287	307	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
308	321	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
322	342	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
343	369	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

1110 / 1110

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

370 / 370

position of stopcodon in wt / mu cDNA

1110 / 1110

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

1110

coding sequence (CDS) position

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

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

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

248569369

original gDNA sequence snippet

CTGCCTAACAATTAATTCACATGTTGTTATTTTACTGCCCT

altered gDNA sequence snippet

CTGCCTAACAATTAATTCACGTGTTGTTATTTTACTGCCCT

original cDNA sequence snippet

CTGCCTAACAATTAATTCACATGTTGTTATTTTACTGCCCT

altered cDNA sequence snippet

CTGCCTAACAATTAATTCACGTGTTGTTATTTTACTGCCCT

wildtype AA sequence

MWQEYYFLNV FFPLLKVCCL TINSHVVILL PWECYHLIWK ILPYIGTTVG SMEEYNTSST
DFTFMGLFNR KETSGLIFAI ISIIFFTALM ANGVMIFLIQ TDLRLHTPMY FLLSHLSLID
MMYISTIVPK MLVNYLLDQR TISFVGCTAQ HFLYLTLVGA EFFLLGLMAY DRYVAICNPL
RYPVLMSRRV CWMIIAGSWF GGSLDGFLLT PITMSFPFCN SREINHFFCE APAVLKLACA
DTALYETVMY VCCVLMLLIP FSVVLASYAR ILTTVQCMSS VEGRKKAFAT CSSHMTVVSL
FYGAAMYTYM LPHSYHKPAQ DKVLSVFYTI LTPMLNPLIY SLRNKDVTGA LKRALGRFKG
PQRVSGGVF*

mutated AA sequence

MWQEYYFLNV FFPLLKVCCL TINSRVVILL PWECYHLIWK ILPYIGTTVG SMEEYNTSST
DFTFMGLFNR KETSGLIFAI ISIIFFTALM ANGVMIFLIQ TDLRLHTPMY FLLSHLSLID
MMYISTIVPK MLVNYLLDQR TISFVGCTAQ HFLYLTLVGA EFFLLGLMAY DRYVAICNPL
RYPVLMSRRV CWMIIAGSWF GGSLDGFLLT PITMSFPFCN SREINHFFCE APAVLKLACA
DTALYETVMY VCCVLMLLIP FSVVLASYAR ILTTVQCMSS VEGRKKAFAT CSSHMTVVSL
FYGAAMYTYM LPHSYHKPAQ DKVLSVFYTI LTPMLNPLIY SLRNKDVTGA LKRALGRFKG
PQRVSGGVF*

speed

0.66 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