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: ENST00000333796
MT speed 0 s - this script 2.623075 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
USP17L2	polymorphism_automatic	0.575225505979884	simple_aae				L62F	single base exchange	rs75476700		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.424774494020116 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr8:11996086G>AN/A show variant in all transcripts IGV

HGNC symbol

USP17L2

Ensembl transcript ID

ENST00000333796

Genbank transcript ID

NM_001256869

UniProt peptide

Q6R6M4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.184C>T
cDNA.501C>T
g.501C>T

AA changes

L62F Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs75476700

database	homozygous (A/A)	heterozygous	allele carriers
1000G	319	634	953
ExAC	4836	17777	22613

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.563	0.971
	-0.035	0.886
(flanking)	-0.086	0.871

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 marginally increased	495	wt: 0.4851 / mu: 0.5358 (marginal change - not scored)	wt: TGGCAAGACAGCTTG mu: TGGCAAGACAGTTTG	GCAA\|gaca

distance from splice site

501

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000029995

Mmulatta

all identical

ENSMMUG00000032404

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000062369

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0260936

151

GWKQ

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1593 / 1593

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

531 / 531

position of stopcodon in wt / mu cDNA

1910 / 1910

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

318 / 318

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

1593

coding sequence (CDS) position

184

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

501

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

501

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

11996086

original gDNA sequence snippet

TGGCTCCTGTGGCAAGACAGCTTGCTCCCAGGAAGAAGCTT

altered gDNA sequence snippet

TGGCTCCTGTGGCAAGACAGTTTGCTCCCAGGAAGAAGCTT

original cDNA sequence snippet

TGGCTCCTGTGGCAAGACAGCTTGCTCCCAGGAAGAAGCTT

altered cDNA sequence snippet

TGGCTCCTGTGGCAAGACAGTTTGCTCCCAGGAAGAAGCTT

wildtype AA sequence

MEDDSLYLGG EWQFNHFSKL TSSRPDAAFA EIQRTSLPEK SPLSSEARVD LCDDLAPVAR
QLAPRKKLPL SSRRPAAVGA GLQNMGNTCY ENASLQCLTY TPPLANYMLS REHSQTCQRP
KCCMLCTMQA HITWALHSPG HVIQPSQALA AGFHRGKQED AHEFLMFTVD AMKKACLPGH
KQVDHHSKDT TLIHQIFGGC WRSQIKCLHC HGISDTFDPY LDIALDIQAA QSVKQALEQL
VKPEELNGEN AYHCGLCLQR APASKTLTLH TSAKVLILVL KRFSDVTGNK LAKNVQYPEC
LDMQPYMSQQ NTGPLVYVLY AVLVHAGWSC HDGHYFSYVK AQEGQWYKMD DAKVTACSIT
SVLSQQAYVL FYIQKSEWER HSESVSRGRE PRALGAEDTD RRATQGELKR DHPCLQAPEL
DERLVERATQ ESTLDHWKFP QEQNKTKPEF NVRKVEGTLP PNVLVIHQSK YKCGMKNHHP
EQQSSLLNLS STTRTDQESV NTGTLASLQG RTRRSKGKNK HSKRALLVCQ *

mutated AA sequence

MEDDSLYLGG EWQFNHFSKL TSSRPDAAFA EIQRTSLPEK SPLSSEARVD LCDDLAPVAR
QFAPRKKLPL SSRRPAAVGA GLQNMGNTCY ENASLQCLTY TPPLANYMLS REHSQTCQRP
KCCMLCTMQA HITWALHSPG HVIQPSQALA AGFHRGKQED AHEFLMFTVD AMKKACLPGH
KQVDHHSKDT TLIHQIFGGC WRSQIKCLHC HGISDTFDPY LDIALDIQAA QSVKQALEQL
VKPEELNGEN AYHCGLCLQR APASKTLTLH TSAKVLILVL KRFSDVTGNK LAKNVQYPEC
LDMQPYMSQQ NTGPLVYVLY AVLVHAGWSC HDGHYFSYVK AQEGQWYKMD DAKVTACSIT
SVLSQQAYVL FYIQKSEWER HSESVSRGRE PRALGAEDTD RRATQGELKR DHPCLQAPEL
DERLVERATQ ESTLDHWKFP QEQNKTKPEF NVRKVEGTLP PNVLVIHQSK YKCGMKNHHP
EQQSSLLNLS STTRTDQESV NTGTLASLQG RTRRSKGKNK HSKRALLVCQ *

speed

0.62 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