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: ENST00000275358
MT speed 0 s - this script 3.341682 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
VWDE	polymorphism_automatic	8.88870905629835e-05	simple_aae		affected		T1032M	single base exchange	rs2053380		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999911112909437 (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)

chr7:12400837G>AN/A show variant in all transcripts IGV

HGNC symbol

VWDE

Ensembl transcript ID

ENST00000275358

Genbank transcript ID

NM_001135924

UniProt peptide

Q8N2E2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3095C>T
cDNA.3284C>T
g.42731C>T

AA changes

T1032M Score: 81 explain score(s)

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

1032

frameshift

known variant

Reference ID: rs2053380

database	homozygous (A/A)	heterozygous	allele carriers
1000G	1518	793	2311
ExAC	6535	3573	10108

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.718	0.987
	1.985	0.986
(flanking)	0.276	0.922

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 increased	42736	wt: 0.34 / mu: 0.37	wt: CGGTCATATATGATG mu: TGGTCATATATGATG	GTCA\|tata

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1032

mutated

not conserved

1032

Ptroglodytes

not conserved

ENSPTRG00000018938

1032

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000011673

1027

Dmelanogaster

no alignment

FBgn0028936

n/a

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1106	1106	CONFLICT	Q -> L (in Ref. 4; BAB55237).	might get lost (downstream of altered splice site)
1177	1216	DOMAIN	EGF-like 1.	might get lost (downstream of altered splice site)
1181	1181	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1183	1183	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1189	1189	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1204	1204	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1206	1206	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1215	1215	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1294	1326	DOMAIN	EGF-like 2.	might get lost (downstream of altered splice site)
1298	1298	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1302	1302	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1308	1308	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1314	1314	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1316	1316	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1325	1325	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1358	1390	DOMAIN	EGF-like 3.	might get lost (downstream of altered splice site)
1362	1362	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1366	1366	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1371	1371	CONFLICT	T -> I (in Ref. 4; BAB55237).	might get lost (downstream of altered splice site)
1372	1372	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1378	1378	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1380	1380	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1389	1389	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1422	1454	DOMAIN	EGF-like 4.	might get lost (downstream of altered splice site)
1426	1426	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1430	1430	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1436	1436	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1442	1442	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1444	1444	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1453	1453	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1455	1486	DOMAIN	EGF-like 5.	might get lost (downstream of altered splice site)
1458	1458	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1462	1462	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1468	1468	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1474	1474	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1518	1550	DOMAIN	EGF-like 6.	might get lost (downstream of altered splice site)
1522	1522	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1526	1526	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1532	1532	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1538	1538	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1540	1540	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1549	1549	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1551	1582	DOMAIN	EGF-like 7.	might get lost (downstream of altered splice site)
1554	1554	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1558	1558	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1564	1564	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1570	1570	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1572	1572	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1581	1581	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4773 / 4773

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

1591 / 1591

position of stopcodon in wt / mu cDNA

4962 / 4962

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

190 / 190

chromosome

strand

-1

last intron/exon boundary

4948

theoretical NMD boundary in CDS

4708

length of CDS

4773

coding sequence (CDS) position

3095

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

3284

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

42731

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

12400837

original gDNA sequence snippet

ATTCAGTAATCCCAAAATAACGGTCATATATGATGGTGCTT

altered gDNA sequence snippet

ATTCAGTAATCCCAAAATAATGGTCATATATGATGGTGCTT

original cDNA sequence snippet

ATTCAGTAATCCCAAAATAACGGTCATATATGATGGTGCTT

altered cDNA sequence snippet

ATTCAGTAATCCCAAAATAATGGTCATATATGATGGTGCTT

wildtype AA sequence

MPGGACVLVI ALMFLAWGEA QECSPGGHQF LRSPYRSVRF DSWHLQQSAV QDLICDHSLS
PGWYRFLILD RPAEMPTKCV EMNHCGTQAP IWLSLRDSET LPSPGEIKQL TACATWQFLF
STTKDCCLFQ IPVSVRNCGN FSVYLLQPTQ GCMGYCAEAI SDARLHPCGS DETETGGDCV
RQLAASLPPP PAGRPEVLVE LIESRLFCRC SFDVPATKNS VGFHIAWSRL SSQEVKEELT
QETTVQAFSL LELDGINLRL GDRIFCSASV FFLENPHVQS VAIESQEFFA GFKLQPELST
ISEDGKEYYL RIESTVPIIC SEFSELDQEC KISLKLKTIG QGREHLGLNL ALSSCHVDLL
QTSSCANGTC SHTFVYYTAV TDFSRDGDRV SNIVVQPIVN EDFLWNNYIP DSIQIKVKDV
PTAYCYTFTD PHIITFDGRV YDNFKTGTFV LYKSMSRDFE VHVRQWDCRS LHYPVSCNCG
FVAQEGGDIV TFDMCNGQLR ESQPYLFIKS QDVTRNIKIS ESYLGRKVTI WFSSGAFIRA
DLGEWGMSLT IRAPSVDYRN TLGLCGTFDE NPENDFHDKN GMQIDQNFNN YVAFINEWRI
LPGKSMSDTL PVSMTSPGKP SYCSCSLDTA AYPSSEDLDS VSRSEIALGC KDLNHVSLSS
LIPELDVTSE YINSDTLVRE INKHTSPEEY NLNLFLQEKK HINLTKLGLN VQKHPGNEKE
DSLQYLANKK YTQGRGSHSQ EMRYNRQNRW KRQNFHEFPP LFAFPSLSQT DLEELTYFFP
EDHAEDVQQE FFPSWPTPSG LTEYSTLTLC QETLANSSIG RLCLAFLGKR LDSVIEMCVK
DVLLKDDLSW AEAGVALLEN ECEKRIVEEG KYNTEEYGTS IEDILSVLKC PNLCSGNGQC
MEWGCACSPS FSSYDCSDSY DKAPEITELG NAGFCDVQKY NCMMVRVFGK GFKELPSIKC
EVTKLQYNSS EWMPGEPIYT QTVFHNSRAV DCQLPTDVQQ FDTMDLVGGK PTGKWQLKVS
NDGYKFSNPK ITVIYDGACQ VCGLYKNDSC TIKENVCIID GLCYVEGDKN PTSPCLICRP
KISRFTWSFL ENNQPPVIQA LQDKLQTFYG ENFEYQFVAF DPEGSDIHFT LDSGPEGASV
SSAGLFMWKT DLLTTQQITV RLNDDCDAET RVTIEVTVKS CDCLNGGSCV SDRNFSPGSG
VYLCVCLPGF HGSLCEVDIS GCQSNPCGLG SYISGFHSYS CDCPPELKVE TQFVNQFTTQ
TVVLTRSDKS VNKEEDDKNA QGRKRHVKPT SGNAFTICKY PCGKSRECVA PNICKCKPGY
IGSNCQTALC DPDCKNHGKC IKPNICQCLP GHGGATCDEE HCNPPCQHGG TCLAGNLCTC
PYGFVGPRCE TMVCNRHCEN GGQCLTPDIC QCKPGWYGPT CSTALCDPVC LNGGSCNKPN
TCLCPNGFFG EHCQNAFCHP PCKNGGHCMR NNVCVCREGY TGRRFQKSIC DPTCMNGGKC
VGPSTCSCPS GWSGKRCNTP ICLQKCKNGG ECIAPSICHC PSSWEGVRCQ IPICNPKCLY
GGRCIFPNVC SCRTEYSGVK CEKKIQIRRH *

mutated AA sequence

MPGGACVLVI ALMFLAWGEA QECSPGGHQF LRSPYRSVRF DSWHLQQSAV QDLICDHSLS
PGWYRFLILD RPAEMPTKCV EMNHCGTQAP IWLSLRDSET LPSPGEIKQL TACATWQFLF
STTKDCCLFQ IPVSVRNCGN FSVYLLQPTQ GCMGYCAEAI SDARLHPCGS DETETGGDCV
RQLAASLPPP PAGRPEVLVE LIESRLFCRC SFDVPATKNS VGFHIAWSRL SSQEVKEELT
QETTVQAFSL LELDGINLRL GDRIFCSASV FFLENPHVQS VAIESQEFFA GFKLQPELST
ISEDGKEYYL RIESTVPIIC SEFSELDQEC KISLKLKTIG QGREHLGLNL ALSSCHVDLL
QTSSCANGTC SHTFVYYTAV TDFSRDGDRV SNIVVQPIVN EDFLWNNYIP DSIQIKVKDV
PTAYCYTFTD PHIITFDGRV YDNFKTGTFV LYKSMSRDFE VHVRQWDCRS LHYPVSCNCG
FVAQEGGDIV TFDMCNGQLR ESQPYLFIKS QDVTRNIKIS ESYLGRKVTI WFSSGAFIRA
DLGEWGMSLT IRAPSVDYRN TLGLCGTFDE NPENDFHDKN GMQIDQNFNN YVAFINEWRI
LPGKSMSDTL PVSMTSPGKP SYCSCSLDTA AYPSSEDLDS VSRSEIALGC KDLNHVSLSS
LIPELDVTSE YINSDTLVRE INKHTSPEEY NLNLFLQEKK HINLTKLGLN VQKHPGNEKE
DSLQYLANKK YTQGRGSHSQ EMRYNRQNRW KRQNFHEFPP LFAFPSLSQT DLEELTYFFP
EDHAEDVQQE FFPSWPTPSG LTEYSTLTLC QETLANSSIG RLCLAFLGKR LDSVIEMCVK
DVLLKDDLSW AEAGVALLEN ECEKRIVEEG KYNTEEYGTS IEDILSVLKC PNLCSGNGQC
MEWGCACSPS FSSYDCSDSY DKAPEITELG NAGFCDVQKY NCMMVRVFGK GFKELPSIKC
EVTKLQYNSS EWMPGEPIYT QTVFHNSRAV DCQLPTDVQQ FDTMDLVGGK PTGKWQLKVS
NDGYKFSNPK IMVIYDGACQ VCGLYKNDSC TIKENVCIID GLCYVEGDKN PTSPCLICRP
KISRFTWSFL ENNQPPVIQA LQDKLQTFYG ENFEYQFVAF DPEGSDIHFT LDSGPEGASV
SSAGLFMWKT DLLTTQQITV RLNDDCDAET RVTIEVTVKS CDCLNGGSCV SDRNFSPGSG
VYLCVCLPGF HGSLCEVDIS GCQSNPCGLG SYISGFHSYS CDCPPELKVE TQFVNQFTTQ
TVVLTRSDKS VNKEEDDKNA QGRKRHVKPT SGNAFTICKY PCGKSRECVA PNICKCKPGY
IGSNCQTALC DPDCKNHGKC IKPNICQCLP GHGGATCDEE HCNPPCQHGG TCLAGNLCTC
PYGFVGPRCE TMVCNRHCEN GGQCLTPDIC QCKPGWYGPT CSTALCDPVC LNGGSCNKPN
TCLCPNGFFG EHCQNAFCHP PCKNGGHCMR NNVCVCREGY TGRRFQKSIC DPTCMNGGKC
VGPSTCSCPS GWSGKRCNTP ICLQKCKNGG ECIAPSICHC PSSWEGVRCQ IPICNPKCLY
GGRCIFPNVC SCRTEYSGVK CEKKIQIRRH *

speed

1.29 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