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: ENST00000374779
MT speed 0 s - this script 2.328954 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR13C5	polymorphism_automatic	3.40140138277434e-11	simple_aae		affected		S18F	single base exchange	rs1851722		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999965986 (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)

chr9:107361642G>AN/A show variant in all transcripts IGV

HGNC symbol

OR13C5

Ensembl transcript ID

ENST00000374779

Genbank transcript ID

NM_001004482

UniProt peptide

Q8NGS8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.53C>T
cDNA.147C>T
g.147C>T

AA changes

S18F Score: 155 explain score(s)

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

frameshift

known variant

Reference ID: rs1851722

database	homozygous (A/A)	heterozygous	allele carriers
1000G	190	825	1015
ExAC	3884	20775	24659

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.081	0
	1.141	0.002
(flanking)	-0.391	0.001

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 increased	149	wt: 0.24 / mu: 0.27	wt: TTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGTTA mu: TTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGTTA	tctg\|GTCA
Acc marginally increased	137	wt: 0.6140 / mu: 0.6644 (marginal change - not scored)	wt: TTCTGGTGGAATTTTTTCTGAAGGGACTTTCTGGTCACCCA mu: TTCTGGTGGAATTTTTTCTGAAGGGACTTTTTGGTCACCCA	ctga\|AGGG
Acc increased	158	wt: 0.34 / mu: 0.47	wt: AGGGACTTTCTGGTCACCCAAGACTTGAGTTACTCTTTTTT mu: AGGGACTTTTTGGTCACCCAAGACTTGAGTTACTCTTTTTT	ccaa\|GACT
Donor marginally increased	138	wt: 0.9252 / mu: 0.9296 (marginal change - not scored)	wt: TCTGAAGGGACTTTC mu: TCTGAAGGGACTTTT	TGAA\|ggga
Acc gained	156	0.31	mu: GAAGGGACTTTTTGGTCACCCAAGACTTGAGTTACTCTTTT	accc\|AAGA

distance from splice site

147

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000029179

Mmulatta

all identical

ENSMMUG00000009754

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
1	25	TOPO_DOM	Extracellular (Potential).	lost
26	46	TRANSMEM	Helical; Name=1; (Potential).	might get lost (downstream of altered splice site)
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	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

1051 / 1051

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

95 / 95

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

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

147

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

147

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

107361642

original gDNA sequence snippet

ATTTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGT

altered gDNA sequence snippet

ATTTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGT

original cDNA sequence snippet

ATTTTTTCTGAAGGGACTTTCTGGTCACCCAAGACTTGAGT

altered cDNA sequence snippet

ATTTTTTCTGAAGGGACTTTTTGGTCACCCAAGACTTGAGT

wildtype AA sequence

MEWENHTILV EFFLKGLSGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY
FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLSLAMGTT ECVLLGVMAF
DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQT VFVVQLPFCR NNIINHFTCE
ILAVMKLACA DISGNEFILL VTTTLFLLTP LLLIIVSYTL IILSIFKISS SEGRSKPSST
CSARLTVVIT FCGTIFLMYM KPKSQETLNS DDLDATDKLI FIFYRVMTPM MNPLIYSLRN
KDVKEAVKHL LRRKNFNK*

mutated AA sequence

MEWENHTILV EFFLKGLFGH PRLELLFFVL IFIMYVVILL GNGTLILISI LDPHLHTPMY
FFLGNLSFLD ICYTTTSIPS TLVSFLSERK TISLSGCAVQ MFLSLAMGTT ECVLLGVMAF
DRYVAICNPL RYPIIMSKDA YVPMAAGSWI IGAVNSAVQT VFVVQLPFCR NNIINHFTCE
ILAVMKLACA DISGNEFILL VTTTLFLLTP LLLIIVSYTL IILSIFKISS SEGRSKPSST
CSARLTVVIT FCGTIFLMYM KPKSQETLNS DDLDATDKLI FIFYRVMTPM MNPLIYSLRN
KDVKEAVKHL LRRKNFNK*

speed

0.32 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