MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000526538
MT speed 0 s - this script 2.13102 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR5M1	polymorphism_automatic	0.014853569596436	simple_aae		affected		S282T	single base exchange	rs4939078		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.985146430403564 (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)

chr11:56380134C>GN/A show variant in all transcripts IGV

HGNC symbol

OR5M1

Ensembl transcript ID

ENST00000526538

Genbank transcript ID

NM_001004740

UniProt peptide

Q8NGP8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.845G>C
cDNA.845G>C
g.845G>C

AA changes

S282T Score: 58 explain score(s)

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

282

frameshift

known variant

Reference ID: rs4939078

database	homozygous (G/G)	heterozygous	allele carriers
1000G	537	1021	1558
ExAC	9816	13135	22951

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.209	0.762
	1.613	0.776
(flanking)	1.855	0.748

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	843	wt: 0.9401 / mu: 0.9487 (marginal change - not scored)	wt: GCAGTCTTTTATACTTTTTTGAGCCCAATGCTGAACCCATT mu: GCAGTCTTTTATACTTTTTTGACCCCAATGCTGAACCCATT	tttg\|AGCC
Acc marginally increased	839	wt: 0.7470 / mu: 0.7636 (marginal change - not scored)	wt: AACTGCAGTCTTTTATACTTTTTTGAGCCCAATGCTGAACC mu: AACTGCAGTCTTTTATACTTTTTTGACCCCAATGCTGAACC	cttt\|TTTG
Acc increased	840	wt: 0.33 / mu: 0.37	wt: ACTGCAGTCTTTTATACTTTTTTGAGCCCAATGCTGAACCC mu: ACTGCAGTCTTTTATACTTTTTTGACCCCAATGCTGAACCC	tttt\|TTGA
Acc increased	850	wt: 0.29 / mu: 0.75	wt: TTTATACTTTTTTGAGCCCAATGCTGAACCCATTGATCTAT mu: TTTATACTTTTTTGACCCCAATGCTGAACCCATTGATCTAT	ccaa\|TGCT
Acc marginally increased	848	wt: 0.8393 / mu: 0.8501 (marginal change - not scored)	wt: CTTTTATACTTTTTTGAGCCCAATGCTGAACCCATTGATCT mu: CTTTTATACTTTTTTGACCCCAATGCTGAACCCATTGATCT	gccc\|AATG
Acc gained	847	0.80	mu: TCTTTTATACTTTTTTGACCCCAATGCTGAACCCATTGATC	accc\|CAAT
Acc gained	849	0.57	mu: TTTTATACTTTTTTGACCCCAATGCTGAACCCATTGATCTA	ccca\|ATGC
Donor gained	846	0.35	mu: TTGACCCCAATGCTG	GACC\|ccaa

distance from splice site

104

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

282

mutated

all conserved

282

Ptroglodytes

all identical

ENSPTRG00000041771

282

Mmulatta

all identical

ENSMMUG00000015393

282

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000057761

282

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
272	292	TRANSMEM	Helical; Name=7; (Potential).	lost
293	315	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

948 / 948

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

316 / 316

position of stopcodon in wt / mu cDNA

948 / 948

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

-1

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

948

coding sequence (CDS) position

845

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

845

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

845

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

56380134

original gDNA sequence snippet

AGTCTTTTATACTTTTTTGAGCCCAATGCTGAACCCATTGA

altered gDNA sequence snippet

AGTCTTTTATACTTTTTTGACCCCAATGCTGAACCCATTGA

original cDNA sequence snippet

AGTCTTTTATACTTTTTTGAGCCCAATGCTGAACCCATTGA

altered cDNA sequence snippet

AGTCTTTTATACTTTTTTGACCCCAATGCTGAACCCATTGA

wildtype AA sequence

MFSPNHTIVT EFILLGLTDD PVLEKILFGV FLAIYLITLA GNLCMILLIR TNSHLQTPMY
FFLGHLSFVD ICYSSNVTPN MLHNFLSEQK TISYAGCFTQ CLLFIALVIT EFYILASMAL
DRYVAICSPL HYSSRMSKNI CVCLVTIPYM YGFLSGFSQS LLTFHLSFCG SLEINHFYCA
DPPLIMLACS DTRVKKMAMF VVAGFNLSSS LFIILLSYLF IFAAIFRIRS AEGRHKAFST
CASHLTIVTL FYGTLFCMYV RPPSEKSVEE SKITAVFYTF LSPMLNPLIY SLRNTDVILA
MQQMIRGKSF HKIAV*

mutated AA sequence

speed

0.11 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