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: ENST00000234347
MT speed 0 s - this script 2.801675 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PRTN3	polymorphism_automatic	8.10596034739319e-12	simple_aae				V119I	single base exchange	rs351111		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999991894 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:844020G>AN/A show variant in all transcripts IGV

HGNC symbol

PRTN3

Ensembl transcript ID

ENST00000234347

Genbank transcript ID

NM_002777

UniProt peptide

P24158

alteration type

single base exchange

alteration region

CDS

DNA changes

c.355G>A
cDNA.390G>A
g.3047G>A

AA changes

V119I Score: 29 explain score(s)

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

119

frameshift

known variant

Reference ID: rs351111

database	homozygous (A/A)	heterozygous	allele carriers
1000G	519	1185	1704
ExAC	11002	10763	21765

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.459	0
	-0.768	0
(flanking)	1.542	0.001

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

119

mutated

all conserved

119

Ptroglodytes

no alignment

ENSPTRG00000023069

n/a

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000057729

121

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000021647

114

protein features

start (aa)	end (aa)	feature	details
28	248	DOMAIN	Peptidase S1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

771 / 771

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

257 / 257

position of stopcodon in wt / mu cDNA

806 / 806

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

36 / 36

chromosome

strand

last intron/exon boundary

636

theoretical NMD boundary in CDS

550

length of CDS

771

coding sequence (CDS) position

355

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

390

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

3047

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

844020

original gDNA sequence snippet

CGGAGAACAAACTGAACGACGTTCTCCTCATCCAGGTGGGC

altered gDNA sequence snippet

CGGAGAACAAACTGAACGACATTCTCCTCATCCAGGTGGGC

original cDNA sequence snippet

CGGAGAACAAACTGAACGACGTTCTCCTCATCCAGCTGAGC

altered cDNA sequence snippet

CGGAGAACAAACTGAACGACATTCTCCTCATCCAGCTGAGC

wildtype AA sequence

MAHRPPSPAL ASVLLALLLS GAARAAEIVG GHEAQPHSRP YMASLQMRGN PGSHFCGGTL
IHPSFVLTAA HCLRDIPQRL VNVVLGAHNV RTQEPTQQHF SVAQVFLNNY DAENKLNDVL
LIQLSSPANL SASVATVQLP QQDQPVPHGT QCLAMGWGRV GAHDPPAQVL QELNVTVVTF
FCRPHNICTF VPRRKAGICF GDSGGPLICD GIIQGIDSFV IWGCATRLFP DFFTRVALYV
DWIRSTLRRV EAKGRP*

mutated AA sequence

MAHRPPSPAL ASVLLALLLS GAARAAEIVG GHEAQPHSRP YMASLQMRGN PGSHFCGGTL
IHPSFVLTAA HCLRDIPQRL VNVVLGAHNV RTQEPTQQHF SVAQVFLNNY DAENKLNDIL
LIQLSSPANL SASVATVQLP QQDQPVPHGT QCLAMGWGRV GAHDPPAQVL QELNVTVVTF
FCRPHNICTF VPRRKAGICF GDSGGPLICD GIIQGIDSFV IWGCATRLFP DFFTRVALYV
DWIRSTLRRV EAKGRP*

speed

0.80 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems