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: ENST00000305899
MT speed 0 s - this script 2.3211 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR10H2	polymorphism_automatic	0.88391002057808	simple_aae		affected		L40Q	single base exchange	rs4569397		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.11608997942192 (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)

chr19:15838972T>AN/A show variant in all transcripts IGV

HGNC symbol

OR10H2

Ensembl transcript ID

ENST00000305899

Genbank transcript ID

NM_013939

UniProt peptide

O60403

alteration type

single base exchange

alteration region

CDS

DNA changes

c.119T>A
cDNA.139T>A
g.139T>A

AA changes

L40Q Score: 113 explain score(s)

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

frameshift

known variant

Reference ID: rs4569397

database	homozygous (A/A)	heterozygous	allele carriers
1000G	238	834	1072
ExAC	5039	22689	27728

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.275	0.999
	1.984	1
(flanking)	2.421	1

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	133	wt: 0.3888 / mu: 0.4073 (marginal change - not scored)	wt: CCTGCTGATGTACCTGTTCACGCTGCTGGGCAACCTGCTCA mu: CCTGCTGATGTACCTGTTCACGCTGCAGGGCAACCTGCTCA	tcac\|GCTG
Donor increased	141	wt: 0.46 / mu: 0.65	wt: TGCTGGGCAACCTGC mu: TGCAGGGCAACCTGC	CTGG\|gcaa
Donor increased	140	wt: 0.30 / mu: 0.54	wt: CTGCTGGGCAACCTG mu: CTGCAGGGCAACCTG	GCTG\|ggca
Donor increased	136	wt: 0.20 / mu: 0.40	wt: CACGCTGCTGGGCAA mu: CACGCTGCAGGGCAA	CGCT\|gctg

distance from splice site

139

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010630

Mmulatta

all identical

ENSMMUG00000014654

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000094891

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
26	46	TRANSMEM	Helical; Name=1; (Potential).	lost
47	54	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
55	75	TRANSMEM	Helical; Name=2; (Potential).	might get lost (downstream of altered splice site)
76	99	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
97	97	DISULFID	By similarity.	might get lost (downstream of altered splice site)
100	120	TRANSMEM	Helical; Name=3; (Potential).	might get lost (downstream of altered splice site)
121	139	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
140	160	TRANSMEM	Helical; Name=4; (Potential).	might get lost (downstream of altered splice site)
161	197	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
189	189	DISULFID	By similarity.	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
219	238	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
239	259	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
260	272	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
273	293	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
294	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

968 / 968

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

21 / 21

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

948

coding sequence (CDS) position

119

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

139

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

139

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

15838972

original gDNA sequence snippet

GATGTACCTGTTCACGCTGCTGGGCAACCTGCTCATCATGG

altered gDNA sequence snippet

GATGTACCTGTTCACGCTGCAGGGCAACCTGCTCATCATGG

original cDNA sequence snippet

GATGTACCTGTTCACGCTGCTGGGCAACCTGCTCATCATGG

altered cDNA sequence snippet

GATGTACCTGTTCACGCTGCAGGGCAACCTGCTCATCATGG

wildtype AA sequence

MLGLNHTSMS EFILVGFSAF PHLQLMLFLL FLLMYLFTLL GNLLIMATVW SERSLHTPMY
LFLCVLSVSE ILYTVAIIPR MLADLLSTQR SIAFLACASQ MFFSFSFGFT HSFLLTVMGY
DRYVAICHPL RYNVLMSPRG CACLVGCSWA GGSVMGMVVT SAIFQLTFCG SHEIQHFLCH
VPPLLKLACG NNVPAVALGV GLVCIMALLG CFLLILLSYA FIVADILKIP SAEGRNKAFS
TCASHLIVVI VHYGFASVIY LKPKGPHSQE GDTLMATTYA VLTPFLSPII FSLRNKELKV
AMKRTFLSTL YSSGT*

mutated AA sequence

MLGLNHTSMS EFILVGFSAF PHLQLMLFLL FLLMYLFTLQ GNLLIMATVW SERSLHTPMY
LFLCVLSVSE ILYTVAIIPR MLADLLSTQR SIAFLACASQ MFFSFSFGFT HSFLLTVMGY
DRYVAICHPL RYNVLMSPRG CACLVGCSWA GGSVMGMVVT SAIFQLTFCG SHEIQHFLCH
VPPLLKLACG NNVPAVALGV GLVCIMALLG CFLLILLSYA FIVADILKIP SAEGRNKAFS
TCASHLIVVI VHYGFASVIY LKPKGPHSQE GDTLMATTYA VLTPFLSPII FSLRNKELKV
AMKRTFLSTL YSSGT*

speed

0.27 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