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: ENST00000542196
MT speed 0 s - this script 2.527326 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR13C2	polymorphism_automatic	2.29816166097407e-14	simple_aae		affected		S160T	single base exchange	rs1851716		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999977 (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)

chr9:107367431A>TN/A show variant in all transcripts IGV

HGNC symbol

OR13C2

Ensembl transcript ID

ENST00000542196

Genbank transcript ID

NM_001004481

UniProt peptide

Q8NGS9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.478T>A
cDNA.521T>A
g.521T>A

AA changes

S160T Score: 58 explain score(s)

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

160

frameshift

known variant

Reference ID: rs1851716

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	6014	20739	26753

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.062	0.04
	2.304	0.049
(flanking)	-0.287	0.016

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
Donor increased	520	wt: 0.61 / mu: 0.77	wt: GTACAATCAGTGTTT mu: GTACAAACAGTGTTT	ACAA\|tcag
Donor increased	518	wt: 0.28 / mu: 0.62	wt: CAGTACAATCAGTGT mu: CAGTACAAACAGTGT	GTAC\|aatc

distance from splice site

508

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

160

mutated

all conserved

160

Ptroglodytes

all conserved

ENSPTRG00000029178

160

Mmulatta

all conserved

ENSMMUG00000009754

160

Fcatus

no homologue

Mmusculus

no homologue

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
140	160	TRANSMEM	Helical; Name=4; (Potential).	lost
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	217	TRANSMEM	Helical; Name=5; (Potential).	might get lost (downstream of altered splice site)
218	237	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
238	258	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
259	277	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
278	298	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
299	318	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

957 / 957

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

319 / 319

position of stopcodon in wt / mu cDNA

1000 / 1000

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

44 / 44

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

957

coding sequence (CDS) position

478

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

521

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

521

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

107367431

original gDNA sequence snippet

CTGTCAATTCTGCAGTACAATCAGTGTTTGTGGTACAATTG

altered gDNA sequence snippet

CTGTCAATTCTGCAGTACAAACAGTGTTTGTGGTACAATTG

original cDNA sequence snippet

CTGTCAATTCTGCAGTACAATCAGTGTTTGTGGTACAATTG

altered cDNA sequence snippet

CTGTCAATTCTGCAGTACAAACAGTGTTTGTGGTACAATTG

wildtype AA sequence

MEWENHTILV EFFLKGLSGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY
FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLGLAMGTT ECVLLGMMAF
DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQS VFVVQLPFCR NNIINHFTCE
ILAVMKLACA DISDNEFIML VATTLFILTP LLLIIVSYTL IIVSIFKISS SEGRSKASST
CSAHLTVVII FYGTILFMYM KPKSKETLNS DDLDATDKII SMFYGVMTPM MNPLIYSLRN
KDVKEAVKHL LNRRFFSK*

mutated AA sequence

MEWENHTILV EFFLKGLSGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY
FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLGLAMGTT ECVLLGMMAF
DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQT VFVVQLPFCR NNIINHFTCE
ILAVMKLACA DISDNEFIML VATTLFILTP LLLIIVSYTL IIVSIFKISS SEGRSKASST
CSAHLTVVII FYGTILFMYM KPKSKETLNS DDLDATDKII SMFYGVMTPM MNPLIYSLRN
KDVKEAVKHL LNRRFFSK*

speed

0.47 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