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: ENST00000316987
MT speed 0 s - this script 2.771833 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR52E4	polymorphism_automatic	2.66610955534929e-10	simple_aae				R228H	single base exchange	rs4757987		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999733389 (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 CM1614793)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:5906205G>AN/A show variant in all transcripts IGV

HGNC symbol

OR52E4

Ensembl transcript ID

ENST00000316987

Genbank transcript ID

NM_001005165

UniProt peptide

Q8NGH9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.683G>A
cDNA.705G>A
g.705G>A

AA changes

R228H Score: 29 explain score(s)

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

228

frameshift

known variant

Reference ID: rs4757987

database	homozygous (A/A)	heterozygous	allele carriers
1000G	453	1209	1662
ExAC	9439	13889	23328

known disease mutation at this position, please check HGMD for details (HGMD ID CM1614793)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.264	0
	0.38	0
(flanking)	-1.286	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	709	wt: 0.6381 / mu: 0.6423 (marginal change - not scored)	wt: CTTAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCCGACT mu: CTTAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCCGACT	cctt\|CCCT
Acc marginally increased	711	wt: 0.9584 / mu: 0.9649 (marginal change - not scored)	wt: TAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCCGACTAA mu: TAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCCGACTAA	ttcc\|CTCT
Acc marginally increased	706	wt: 0.3350 / mu: 0.3559 (marginal change - not scored)	wt: ATCCTTAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCCG mu: ATCCTTAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCCG	tcgc\|CTTC
Acc marginally increased	708	wt: 0.8982 / mu: 0.9375 (marginal change - not scored)	wt: CCTTAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCCGAC mu: CCTTAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCCGAC	gcct\|TCCC

distance from splice site

323

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

228

mutated

not conserved

228

Ptroglodytes

all identical

ENSPTRG00000003268

228

Mmulatta

all identical

ENSMMUG00000008279

228

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000073914

228

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
219	238	TOPO_DOM	Cytoplasmic (Potential).	lost

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

961 / 961

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

23 / 23

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

683

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

705

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

705

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

5906205

original gDNA sequence snippet

TATCCTTAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCC

altered gDNA sequence snippet

TATCCTTAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCC

original cDNA sequence snippet

TATCCTTAGAGCTGTTTTTCGCCTTCCCTCTCAAGATGTCC

altered cDNA sequence snippet

TATCCTTAGAGCTGTTTTTCACCTTCCCTCTCAAGATGTCC

wildtype AA sequence

MPSINDTHFY PPFFLLLGIP GLDTLHIWIS FPFCIVYLIA IVGNMTILFV IKTEHSLHQP
MFYFLAMLSM IDLGLSTSTI PKMLGIFWFN LQEISFGGCL LQMFFIHMFT GMETVLLVVM
AYDRFVAICN PLQYTMILTN KTISILASVV VGRNLVLVTP FVFLILRLPF CGHNIVPHTY
CEHRGLAGLA CAPIKINIIY GLMVISYIIV DVILIASSYV LILRAVFRLP SQDVRLKAFN
TCGSHVCVML CFYTPAFFSF MTHRFGQNIP HYIHILLANL YVVVPPALNP VIYGVRTKQI
REQIVKIFVQ KE*

mutated AA sequence

MPSINDTHFY PPFFLLLGIP GLDTLHIWIS FPFCIVYLIA IVGNMTILFV IKTEHSLHQP
MFYFLAMLSM IDLGLSTSTI PKMLGIFWFN LQEISFGGCL LQMFFIHMFT GMETVLLVVM
AYDRFVAICN PLQYTMILTN KTISILASVV VGRNLVLVTP FVFLILRLPF CGHNIVPHTY
CEHRGLAGLA CAPIKINIIY GLMVISYIIV DVILIASSYV LILRAVFHLP SQDVRLKAFN
TCGSHVCVML CFYTPAFFSF MTHRFGQNIP HYIHILLANL YVVVPPALNP VIYGVRTKQI
REQIVKIFVQ KE*

speed

0.77 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