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: ENST00000409379
MT speed 0 s - this script 2.874645 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TONSL	polymorphism_automatic	1.07704719587431e-08	simple_aae		affected		A714V	single base exchange	rs7830832		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999989229528 (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)

chr8:145661675G>AN/A show variant in all transcripts IGV

HGNC symbol

TONSL

Ensembl transcript ID

ENST00000409379

Genbank transcript ID

NM_013432

UniProt peptide

Q96HA7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2141C>T
cDNA.2171C>T
g.8153C>T

AA changes

A714V Score: 64 explain score(s)

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

714

frameshift

known variant

Reference ID: rs7830832

database	homozygous (A/A)	heterozygous	allele carriers
1000G	530	1155	1685
ExAC	10957	10853	21810

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.319	0.026
	1.323	0.038
(flanking)	1.135	0.035

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	8161	wt: 0.37 / mu: 0.54	wt: AGGCCTCTCAGGCCCATGTCAGGGTCTCCCCAGGGCAGGCG mu: AGGCCTCTCAGGTCCATGTCAGGGTCTCCCCAGGGCAGGCG	gtca\|GGGT
Donor marginally increased	8157	wt: 0.9056 / mu: 0.9561 (marginal change - not scored)	wt: GCCCATGTCAGGGTC mu: GTCCATGTCAGGGTC	CCAT\|gtca
Donor gained	8146	0.62	mu: AGGCCTCTCAGGTCC	GCCT\|ctca

distance from splice site

127

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

714

mutated

not conserved

714

Ptroglodytes

all identical

ENSPTRG00000020702

714

Mmulatta

all identical

ENSMMUG00000002655

559

Fcatus

all identical

ENSFCAG00000014379

553

Mmusculus

all identical

ENSMUSG00000059323

714

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000007494

n/a

Drerio

not conserved

ENSDARG00000071294

713

Dmelanogaster

not conserved

FBgn0035812

698

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000020475

696

protein features

start (aa)	end (aa)	feature	details
719	719	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1069	1093	REPEAT	LRR 1.	might get lost (downstream of altered splice site)
1097	1122	REPEAT	LRR 2.	might get lost (downstream of altered splice site)
1128	1151	REPEAT	LRR 3.	might get lost (downstream of altered splice site)
1188	1212	REPEAT	LRR 4.	might get lost (downstream of altered splice site)
1247	1270	REPEAT	LRR 5.	might get lost (downstream of altered splice site)
1275	1300	REPEAT	LRR 6.	might get lost (downstream of altered splice site)
1331	1354	REPEAT	LRR 7.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4137 / 4137

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

1379 / 1379

position of stopcodon in wt / mu cDNA

4167 / 4167

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

31 / 31

chromosome

strand

-1

last intron/exon boundary

3974

theoretical NMD boundary in CDS

3893

length of CDS

4137

coding sequence (CDS) position

2141

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

2171

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

8153

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

145661675

original gDNA sequence snippet

ACTCCCAGAGGCCTCTCAGGCCCATGTCAGGGTCTCCCCAG

altered gDNA sequence snippet

ACTCCCAGAGGCCTCTCAGGTCCATGTCAGGGTCTCCCCAG

original cDNA sequence snippet

ACTCCCAGAGGCCTCTCAGGCCCATGTCAGGGTCTCCCCAG

altered cDNA sequence snippet

ACTCCCAGAGGCCTCTCAGGTCCATGTCAGGGTCTCCCCAG

wildtype AA sequence

MSLERELRQL SKAKAKAQRA GQRREEAALC HQLGELLAGH GRYAEALEQH WQELQLRERA
DDPLGCAVAH RKIGERLAEM EDYPAALQHQ HQYLELAHSL RNHTELQRAW ATIGRTHLDI
YDHCQSRDAL LQAQAAFEKS LAIVDEELEG TLAQGELNEM RTRLYLNLGL TFESLQQTAL
CNDYFRKSIF LAEQNHLYED LFRARYNLGT IHWRAGQHSQ AMRCLEGARE CAHTMRKRFM
ESECCVVIAQ VLQDLGDFLA AKRALKKAYR LGSQKPVQRA AICQNLQHVL AVVRLQQQLE
EAEGRDPQGA MVICEQLGDL FSKAGDFPRA AEAYQKQLRF AELLDRPGAE RAIIHVSLAT
TLGDMKDHHG AVRHYEEELR LRSGNVLEEA KTWLNIALSR EEAGDAYELL APCFQKALSC
AQQAQRPQLQ RQVLQHLHTV QLRLQPQEAP ETETRLRELS VAEDEDEEEE AEEAAATAES
EALEAGEVEL SEGEDDTDGL TPQLEEDEEL QGHLGRRKGS KWNRRNDMGE TLLHRACIEG
QLRRVQDLVR QGHPLNPRDY CGWTPLHEAC NYGHLEIVRF LLDHGAAVDD PGGQGCEGIT
PLHDALNCGH FEVAELLLER GASVTLRTRK GLSPLETLQQ WVKLYRRDLD LETRQKARAM
EMLLQAAASG QDPHSSQAFH TPSSLLFDPE TSPPLSPCPE PPSNSTRLPE ASQAHVRVSP
GQAAPAMARP RRSRHGPASS SSSSEGEDSA GPARPSQKRP RCSATAQRVA AWTPGPASNR
EAATASTSRA AYQAAIRGVG SAQSRLGPGP PRGHSKALAP QAALIPEEEC LAGDWLELDM
PLTRSRRPRP RGTGDNRRPS STSGSDSEES RPRARAKQVR LTCMQSCSAP VNAGPSSLAS
EPPGSPSTPR VSEPSGDSSA AGQPLGPAPP PPIRVRVQVQ DHLFLIPVPH SSDTHSVAWL
AEQAAQRYYQ TCGLLPRLTL RKEGALLAPQ DLIPDVLQSN DEVLAEVTSW DLPPLTDRYR
RACQSLGQGE HQQVLQAVEL QGLGLSFSAC SLALDQAQLT PLLRALKLHT ALRELRLAGN
RLGDKCVAEL VAALGTMPSL ALLDLSSNHL GPEGLRQLAM GLPGQATLQS LEELDLSMNP
LGDGCGQSLA SLLHACPLLS TLRLQACGFG PSFFLSHQTA LGSAFQDAEH LKTLSLSYNA
LGAPALARTL QSLPAGTLLH LELSSVAAGK GDSDLMEPVF RYLAKEGCAL AHLTLSANHL
GDKAVRDLCR CLSLCPSLIS LDLSANPEIS CASLEELLST LQKRPQGLSF LGLSGCAVQG
PLGLGLWDKI AAQLRELQLC SRRLCAEDRD ALRQLQPSRP GPGECTLDHG SKLFFRRL*

mutated AA sequence

MSLERELRQL SKAKAKAQRA GQRREEAALC HQLGELLAGH GRYAEALEQH WQELQLRERA
DDPLGCAVAH RKIGERLAEM EDYPAALQHQ HQYLELAHSL RNHTELQRAW ATIGRTHLDI
YDHCQSRDAL LQAQAAFEKS LAIVDEELEG TLAQGELNEM RTRLYLNLGL TFESLQQTAL
CNDYFRKSIF LAEQNHLYED LFRARYNLGT IHWRAGQHSQ AMRCLEGARE CAHTMRKRFM
ESECCVVIAQ VLQDLGDFLA AKRALKKAYR LGSQKPVQRA AICQNLQHVL AVVRLQQQLE
EAEGRDPQGA MVICEQLGDL FSKAGDFPRA AEAYQKQLRF AELLDRPGAE RAIIHVSLAT
TLGDMKDHHG AVRHYEEELR LRSGNVLEEA KTWLNIALSR EEAGDAYELL APCFQKALSC
AQQAQRPQLQ RQVLQHLHTV QLRLQPQEAP ETETRLRELS VAEDEDEEEE AEEAAATAES
EALEAGEVEL SEGEDDTDGL TPQLEEDEEL QGHLGRRKGS KWNRRNDMGE TLLHRACIEG
QLRRVQDLVR QGHPLNPRDY CGWTPLHEAC NYGHLEIVRF LLDHGAAVDD PGGQGCEGIT
PLHDALNCGH FEVAELLLER GASVTLRTRK GLSPLETLQQ WVKLYRRDLD LETRQKARAM
EMLLQAAASG QDPHSSQAFH TPSSLLFDPE TSPPLSPCPE PPSNSTRLPE ASQVHVRVSP
GQAAPAMARP RRSRHGPASS SSSSEGEDSA GPARPSQKRP RCSATAQRVA AWTPGPASNR
EAATASTSRA AYQAAIRGVG SAQSRLGPGP PRGHSKALAP QAALIPEEEC LAGDWLELDM
PLTRSRRPRP RGTGDNRRPS STSGSDSEES RPRARAKQVR LTCMQSCSAP VNAGPSSLAS
EPPGSPSTPR VSEPSGDSSA AGQPLGPAPP PPIRVRVQVQ DHLFLIPVPH SSDTHSVAWL
AEQAAQRYYQ TCGLLPRLTL RKEGALLAPQ DLIPDVLQSN DEVLAEVTSW DLPPLTDRYR
RACQSLGQGE HQQVLQAVEL QGLGLSFSAC SLALDQAQLT PLLRALKLHT ALRELRLAGN
RLGDKCVAEL VAALGTMPSL ALLDLSSNHL GPEGLRQLAM GLPGQATLQS LEELDLSMNP
LGDGCGQSLA SLLHACPLLS TLRLQACGFG PSFFLSHQTA LGSAFQDAEH LKTLSLSYNA
LGAPALARTL QSLPAGTLLH LELSSVAAGK GDSDLMEPVF RYLAKEGCAL AHLTLSANHL
GDKAVRDLCR CLSLCPSLIS LDLSANPEIS CASLEELLST LQKRPQGLSF LGLSGCAVQG
PLGLGLWDKI AAQLRELQLC SRRLCAEDRD ALRQLQPSRP GPGECTLDHG SKLFFRRL*

speed

0.81 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