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: ENST00000301364
MT speed 0 s - this script 3.182592 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TSR1	polymorphism_automatic	8.59967198210132e-05	simple_aae		affected		S386G	single base exchange	rs2281726		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999914003280179 (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)

chr17:2236404T>CN/A show variant in all transcripts IGV

HGNC symbol

TSR1

Ensembl transcript ID

ENST00000301364

Genbank transcript ID

NM_018128

UniProt peptide

Q2NL82

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1156A>G
cDNA.2236A>G
g.4398A>G

AA changes

S386G Score: 56 explain score(s)

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

386

frameshift

known variant

Reference ID: rs2281726

database	homozygous (C/C)	heterozygous	allele carriers
1000G	167	535	702
ExAC	1924	13404	15328

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.948	0.463
	0.426	0.613
(flanking)	1.161	0.925

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	4390	wt: 0.49 / mu: 0.64	wt: TTGGGCTTTTACAGATTTCTTGAAGGAAAGTTCTAAGGTGG mu: TTGGGCTTTTACAGATTTCTTGAAGGAAGGTTCTAAGGTGG	tctt\|GAAG
Acc increased	4391	wt: 0.30 / mu: 0.36	wt: TGGGCTTTTACAGATTTCTTGAAGGAAAGTTCTAAGGTGGT mu: TGGGCTTTTACAGATTTCTTGAAGGAAGGTTCTAAGGTGGT	cttg\|AAGG
Donor gained	4392	0.97	mu: TCTTGAAGGAAGGTT	TTGA\|agga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

386

mutated

not conserved

386

Ptroglodytes

all identical

ENSPTRG00000008547

386

Mmulatta

all identical

ENSMMUG00000017519

386

Fcatus

no alignment

ENSFCAG00000006313

n/a

Mmusculus

not conserved

ENSMUSG00000038335

386

Ggallus

all conserved

ENSGALG00000003180

381

Trubripes

not conserved

ENSTRUG00000004665

401

Drerio

not conserved

ENSDARG00000007744

397

Dmelanogaster

not conserved

FBgn0037073

375

Celegans

not conserved

F10G7.1

363

Xtropicalis

all conserved

ENSXETG00000023797

392

protein features

start (aa)	end (aa)	feature	details
415	487	COMPBIAS	Glu-rich.	might get lost (downstream of altered splice site)
475	475	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
737	737	CONFLICT	R -> W (in Ref. 1; BAA92639).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2415 / 2415

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

805 / 805

position of stopcodon in wt / mu cDNA

3495 / 3495

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

1081 / 1081

chromosome

strand

-1

last intron/exon boundary

3317

theoretical NMD boundary in CDS

2186

length of CDS

2415

coding sequence (CDS) position

1156

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

2236

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

4398

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

2236404

original gDNA sequence snippet

TTACAGATTTCTTGAAGGAAAGTTCTAAGGTGGTAAAGAAG

altered gDNA sequence snippet

TTACAGATTTCTTGAAGGAAGGTTCTAAGGTGGTAAAGAAG

original cDNA sequence snippet

CAAAGGATTTCTTGAAGGAAAGTTCTAAGGTGGTAAAGAAG

altered cDNA sequence snippet

CAAAGGATTTCTTGAAGGAAGGTTCTAAGGTGGTAAAGAAG

wildtype AA sequence

MAAHRPGPLK QQNKAHKGGR HRGRGSAQRD GKGRLALKTL SKKVRKELSR VDQRHRASQL
RKQKKEAVLA EKRQLGGKDG PPHQVLVVPL HSRISLPEAM QLLQDRDTGT VHLNELGNTQ
NFMLLCPRLK HRWFFTSARP GDLHVVLDMA KVADTILFLL DPLEGWDSTG DYCLSCLFAQ
GLPTYTLAVQ GISGLPLKKQ IDTRKKLSKA VEKRFPHDKL LLLDTQQEAG MLLRQLANQK
QQHLAFRDRR AYLFAHAVDF VPSEENNLVG TLKISGYVRG QTLNVNRLLH IVGYGDFQMK
QIDAPGDPFP LNPRGIKPQK DPDMAMEICA TDAVDDMEEG LKVLMKADPG RQESLQAEVI
PDPMEGEQTW PTEEELSEAK DFLKESSKVV KKVPKGTSSY QAEWILDGGS QSGGEGDEYE
YDDMEHEDFM EEESQDESSE EEEEYETMTI GESVHDDLYD KKVDEEAEAK MLEKYKQERL
EEMFPDEVDT PRDVAARIRF QKYRGLKSFR TSPWDPKENL PQDYARIFQF QNFTNTRKSI
FKEVEEKEVE GAEVGWYVTL HVSEVPVSVV ECFRQGTPLI AFSLLPHEQK MSVLNMVVRR
DPGNTEPVKA KEELIFHCGF RRFRASPLFS QHTAADKHKL QRFLTADMAL VATVYAPITF
PPASVLLFKQ KSNGMHSLIA TGHLMSVDPD RMVIKRVVLS GHPFKIFTKM AVVRYMFFNR
EDVLWFKPVE LRTKWGRRGH IKEPLGTHGH MKCSFDGKLK SQDTVLMNLY KRVFPKWTYD
PYVPEPVPWL KSEISSTVPQ GGME*

mutated AA sequence

MAAHRPGPLK QQNKAHKGGR HRGRGSAQRD GKGRLALKTL SKKVRKELSR VDQRHRASQL
RKQKKEAVLA EKRQLGGKDG PPHQVLVVPL HSRISLPEAM QLLQDRDTGT VHLNELGNTQ
NFMLLCPRLK HRWFFTSARP GDLHVVLDMA KVADTILFLL DPLEGWDSTG DYCLSCLFAQ
GLPTYTLAVQ GISGLPLKKQ IDTRKKLSKA VEKRFPHDKL LLLDTQQEAG MLLRQLANQK
QQHLAFRDRR AYLFAHAVDF VPSEENNLVG TLKISGYVRG QTLNVNRLLH IVGYGDFQMK
QIDAPGDPFP LNPRGIKPQK DPDMAMEICA TDAVDDMEEG LKVLMKADPG RQESLQAEVI
PDPMEGEQTW PTEEELSEAK DFLKEGSKVV KKVPKGTSSY QAEWILDGGS QSGGEGDEYE
YDDMEHEDFM EEESQDESSE EEEEYETMTI GESVHDDLYD KKVDEEAEAK MLEKYKQERL
EEMFPDEVDT PRDVAARIRF QKYRGLKSFR TSPWDPKENL PQDYARIFQF QNFTNTRKSI
FKEVEEKEVE GAEVGWYVTL HVSEVPVSVV ECFRQGTPLI AFSLLPHEQK MSVLNMVVRR
DPGNTEPVKA KEELIFHCGF RRFRASPLFS QHTAADKHKL QRFLTADMAL VATVYAPITF
PPASVLLFKQ KSNGMHSLIA TGHLMSVDPD RMVIKRVVLS GHPFKIFTKM AVVRYMFFNR
EDVLWFKPVE LRTKWGRRGH IKEPLGTHGH MKCSFDGKLK SQDTVLMNLY KRVFPKWTYD
PYVPEPVPWL KSEISSTVPQ GGME*

speed

0.82 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