Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000392982
Querying Taster for transcript #2: ENST00000298715
MT speed 3.17 s - this script 6.191137 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
VWA2polymorphism_automatic6.16280204801534e-06simple_aaeaffectedA9Tsingle base exchangers9664945show file
VWA2polymorphism_automatic6.16280204801534e-06simple_aaeaffectedA9Tsingle base exchangers9664945show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999993837197952 (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) chr10:116008497G>AN/A show variant in all transcripts   IGV
HGNC symbol VWA2
Ensembl transcript ID ENST00000392982
Genbank transcript ID N/A
UniProt peptide Q5GFL6
alteration type single base exchange
alteration region CDS
DNA changes c.25G>A
cDNA.275G>A
g.9409G>A
AA changes A9T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
9
frameshift no
known variant Reference ID: rs9664945
databasehomozygous (A/A)heterozygousallele carriers
1000G156706862
ExAC28701918522055
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8160.921
0.1550.19
(flanking)-0.1810.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased9406wt: 0.8456 / mu: 0.8844 (marginal change - not scored)wt: TGCCCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTG
mu: TGCCCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTG
 ctgg|AAGC
Acc marginally increased9399wt: 0.8306 / mu: 0.8457 (marginal change - not scored)wt: ATCAACATGCCCCCTTTCCTGTTGCTGGAAGCCGTCTGTGT
mu: ATCAACATGCCCCCTTTCCTGTTGCTGGAAACCGTCTGTGT
 cctg|TTGC
Donor gained94040.55mu: GTTGCTGGAAACCGT TGCT|ggaa
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MPPFLLLEAVCVFLFSRVPPS
mutated  not conserved    9 MPPFLLLETVCVFLFSRVPPSL
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000025082  9 MPPLLLLPAIYMLLFFRVSPTI
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000012019  n/a
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123SIGNALPotential.lost
51222DOMAINVWFA 1.might get lost (downstream of altered splice site)
7676CONFLICTT -> A (in Ref. 3; BAC87116).might get lost (downstream of altered splice site)
147147CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
267268SITECleavage.might get lost (downstream of altered splice site)
296333DOMAINEGF-like 1.might get lost (downstream of altered splice site)
299299DISULFIDBy similarity.might get lost (downstream of altered splice site)
304304DISULFIDBy similarity.might get lost (downstream of altered splice site)
310310DISULFIDBy similarity.might get lost (downstream of altered splice site)
320320DISULFIDBy similarity.might get lost (downstream of altered splice site)
322322DISULFIDBy similarity.might get lost (downstream of altered splice site)
332332DISULFIDBy similarity.might get lost (downstream of altered splice site)
343517DOMAINVWFA 2.might get lost (downstream of altered splice site)
428428CONFLICTQ -> R (in Ref. 1; CAD60276).might get lost (downstream of altered splice site)
531705DOMAINVWFA 3.might get lost (downstream of altered splice site)
712748DOMAINEGF-like 2.might get lost (downstream of altered splice site)
716716DISULFIDBy similarity.might get lost (downstream of altered splice site)
721721DISULFIDBy similarity.might get lost (downstream of altered splice site)
727727DISULFIDBy similarity.might get lost (downstream of altered splice site)
736736DISULFIDBy similarity.might get lost (downstream of altered splice site)
738738DISULFIDBy similarity.might get lost (downstream of altered splice site)
747747DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2268 / 2268
position (AA) of stopcodon in wt / mu AA sequence 756 / 756
position of stopcodon in wt / mu cDNA 2518 / 2518
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 251 / 251
chromosome 10
strand 1
last intron/exon boundary 2499
theoretical NMD boundary in CDS 2198
length of CDS 2268
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)
275
gDNA position
(for ins/del: last normal base / first normal base)
9409
chromosomal position
(for ins/del: last normal base / first normal base)
116008497
original gDNA sequence snippet CCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTGTTT
altered gDNA sequence snippet CCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTGTTT
original cDNA sequence snippet CCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTGTTT
altered cDNA sequence snippet CCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTGTTT
wildtype AA sequence MPPFLLLEAV CVFLFSRVPP SLPLQEVHVS KETIGKISAA SKMMWCSAAV DIMFLLDGSN
SVGKGSFERS KHFAITVCDG LDISPERVRV GAFQFSSTPH LEFPLDSFST QQEVKARIKR
MVFKGGRTET ELALKYLLHR GLPGGRNASV PQILIIVTDG KSQGDVALPS KQLKERGVTV
FAVGVRFPRW EELHALASEP RGQHVLLAEQ VEDATNGLFS TLSSSAICSS ATPDCRVEAH
PCEHRTLEMV REFAGNAPCW RGSRRTLAVL AAHCPFYSWK RVFLTHPATC YRTTCPGPCD
SQPCQNGGTC VPEGLDGYQC LCPLAFGGEA NCALKLSLEC RVDLLFLLDS SAGTTLDGFL
RAKVFVKRFV RAVLSEDSRA RVGVATYSRE LLVAVPVGEY QDVPDLVWSL DGIPFRGGPT
LTGSALRQAA ERGFGSATRT GQDRPRRVVV LLTESHSEDE VAGPARHARA RELLLLGVGS
EAVRAELEEI TGSPKHVMVY SDPQDLFNQI PELQGKLCSR QRPGCRTQAL DLVFMLDTSA
SVGPENFAQM QSFVRSCALQ FEVNPDVTQV GLVVYGSQVQ TAFGLDTKPT RAAMLRAISQ
APYLGGVGSA GTALLHIYDK VMTVQRGARP GVPKAVVVLT GGRGAEDAAV PAQKLRNNGI
SVLVVGVGPV LSEGLRRLAG PRDSLIHVAA YADLRYHQDV LIEWLCGEAK QPVNLCKPSP
CMNEGSCVLQ NGSYRCKCRD GWEGPHCENR FLRRP*
mutated AA sequence MPPFLLLETV CVFLFSRVPP SLPLQEVHVS KETIGKISAA SKMMWCSAAV DIMFLLDGSN
SVGKGSFERS KHFAITVCDG LDISPERVRV GAFQFSSTPH LEFPLDSFST QQEVKARIKR
MVFKGGRTET ELALKYLLHR GLPGGRNASV PQILIIVTDG KSQGDVALPS KQLKERGVTV
FAVGVRFPRW EELHALASEP RGQHVLLAEQ VEDATNGLFS TLSSSAICSS ATPDCRVEAH
PCEHRTLEMV REFAGNAPCW RGSRRTLAVL AAHCPFYSWK RVFLTHPATC YRTTCPGPCD
SQPCQNGGTC VPEGLDGYQC LCPLAFGGEA NCALKLSLEC RVDLLFLLDS SAGTTLDGFL
RAKVFVKRFV RAVLSEDSRA RVGVATYSRE LLVAVPVGEY QDVPDLVWSL DGIPFRGGPT
LTGSALRQAA ERGFGSATRT GQDRPRRVVV LLTESHSEDE VAGPARHARA RELLLLGVGS
EAVRAELEEI TGSPKHVMVY SDPQDLFNQI PELQGKLCSR QRPGCRTQAL DLVFMLDTSA
SVGPENFAQM QSFVRSCALQ FEVNPDVTQV GLVVYGSQVQ TAFGLDTKPT RAAMLRAISQ
APYLGGVGSA GTALLHIYDK VMTVQRGARP GVPKAVVVLT GGRGAEDAAV PAQKLRNNGI
SVLVVGVGPV LSEGLRRLAG PRDSLIHVAA YADLRYHQDV LIEWLCGEAK QPVNLCKPSP
CMNEGSCVLQ NGSYRCKCRD GWEGPHCENR FLRRP*
speed 1.52 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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999993837197952 (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) chr10:116008497G>AN/A show variant in all transcripts   IGV
HGNC symbol VWA2
Ensembl transcript ID ENST00000298715
Genbank transcript ID NM_198496
UniProt peptide Q5GFL6
alteration type single base exchange
alteration region CDS
DNA changes c.25G>A
cDNA.275G>A
g.9409G>A
AA changes A9T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
9
frameshift no
known variant Reference ID: rs9664945
databasehomozygous (A/A)heterozygousallele carriers
1000G156706862
ExAC28701918522055
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.8160.921
0.1550.19
(flanking)-0.1810.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased9406wt: 0.8456 / mu: 0.8844 (marginal change - not scored)wt: TGCCCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTG
mu: TGCCCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTG
 ctgg|AAGC
Acc marginally increased9399wt: 0.8306 / mu: 0.8457 (marginal change - not scored)wt: ATCAACATGCCCCCTTTCCTGTTGCTGGAAGCCGTCTGTGT
mu: ATCAACATGCCCCCTTTCCTGTTGCTGGAAACCGTCTGTGT
 cctg|TTGC
Donor gained94040.55mu: GTTGCTGGAAACCGT TGCT|ggaa
distance from splice site 28
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MPPFLLLEAVCVFLFSRVPPS
mutated  not conserved    9 MPPFLLLETVCVFLFSRVPPSL
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000025082  9 MPPLLLLPAIYMLLFFRVSPTI
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000012019  n/a
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
123SIGNALPotential.lost
51222DOMAINVWFA 1.might get lost (downstream of altered splice site)
7676CONFLICTT -> A (in Ref. 3; BAC87116).might get lost (downstream of altered splice site)
147147CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
267268SITECleavage.might get lost (downstream of altered splice site)
296333DOMAINEGF-like 1.might get lost (downstream of altered splice site)
299299DISULFIDBy similarity.might get lost (downstream of altered splice site)
304304DISULFIDBy similarity.might get lost (downstream of altered splice site)
310310DISULFIDBy similarity.might get lost (downstream of altered splice site)
320320DISULFIDBy similarity.might get lost (downstream of altered splice site)
322322DISULFIDBy similarity.might get lost (downstream of altered splice site)
332332DISULFIDBy similarity.might get lost (downstream of altered splice site)
343517DOMAINVWFA 2.might get lost (downstream of altered splice site)
428428CONFLICTQ -> R (in Ref. 1; CAD60276).might get lost (downstream of altered splice site)
531705DOMAINVWFA 3.might get lost (downstream of altered splice site)
712748DOMAINEGF-like 2.might get lost (downstream of altered splice site)
716716DISULFIDBy similarity.might get lost (downstream of altered splice site)
721721DISULFIDBy similarity.might get lost (downstream of altered splice site)
727727DISULFIDBy similarity.might get lost (downstream of altered splice site)
736736DISULFIDBy similarity.might get lost (downstream of altered splice site)
738738DISULFIDBy similarity.might get lost (downstream of altered splice site)
747747DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2178 / 2178
position (AA) of stopcodon in wt / mu AA sequence 726 / 726
position of stopcodon in wt / mu cDNA 2428 / 2428
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 251 / 251
chromosome 10
strand 1
last intron/exon boundary 1821
theoretical NMD boundary in CDS 1520
length of CDS 2178
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)
275
gDNA position
(for ins/del: last normal base / first normal base)
9409
chromosomal position
(for ins/del: last normal base / first normal base)
116008497
original gDNA sequence snippet CCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTGTTT
altered gDNA sequence snippet CCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTGTTT
original cDNA sequence snippet CCCCTTTCCTGTTGCTGGAAGCCGTCTGTGTTTTCCTGTTT
altered cDNA sequence snippet CCCCTTTCCTGTTGCTGGAAACCGTCTGTGTTTTCCTGTTT
wildtype AA sequence MPPFLLLEAV CVFLFSRVPP SLPLQEVHVS KETIGKISAA SKMMWCSAAV DIMFLLDGSN
SVGKGSFERS KHFAITVCDG LDISPERVRV GAFQFSSTPH LEFPLDSFST QQEVKARIKR
MVFKGGRTET ELALKYLLHR GLPGGRNASV PQILIIVTDG KSQGDVALPS KQLKERGVTV
FAVGVRFPRW EELHALASEP RGQHVLLAEQ VEDATNGLFS TLSSSAICSS ATPDCRVEAH
PCEHRTLEMV REFAGNAPCW RGSRRTLAVL AAHCPFYSWK RVFLTHPATC YRTTCPGPCD
SQPCQNGGTC VPEGLDGYQC LCPLAFGGEA NCALKLSLEC RVDLLFLLDS SAGTTLDGFL
RAKVFVKRFV RAVLSEDSRA RVGVATYSRE LLVAVPVGEY QDVPDLVWSL DGIPFRGGPT
LTGSALRQAA ERGFGSATRT GQDRPRRVVV LLTESHSEDE VAGPARHARA RELLLLGVGS
EAVRAELEEI TGSPKHVMVY SDPQDLFNQI PELQGKLCSR QRPGCRTQAL DLVFMLDTSA
SVGPENFAQM QSFVRSCALQ FEVNPDVTQV GLVVYGSQVQ TAFGLDTKPT RAAMLRAISQ
APYLGGVGSA GTALLHIYDK VMTVQRGARP GVPKAVVVLT GGRGAEDAAV PAQKLRNNGI
SVLVVGVGPV LSEGLRRLAG PRDSLIHVAA YADLRYHQDV LIEWLCGGEW GNPHPQGCPH
GRPSA*
mutated AA sequence MPPFLLLETV CVFLFSRVPP SLPLQEVHVS KETIGKISAA SKMMWCSAAV DIMFLLDGSN
SVGKGSFERS KHFAITVCDG LDISPERVRV GAFQFSSTPH LEFPLDSFST QQEVKARIKR
MVFKGGRTET ELALKYLLHR GLPGGRNASV PQILIIVTDG KSQGDVALPS KQLKERGVTV
FAVGVRFPRW EELHALASEP RGQHVLLAEQ VEDATNGLFS TLSSSAICSS ATPDCRVEAH
PCEHRTLEMV REFAGNAPCW RGSRRTLAVL AAHCPFYSWK RVFLTHPATC YRTTCPGPCD
SQPCQNGGTC VPEGLDGYQC LCPLAFGGEA NCALKLSLEC RVDLLFLLDS SAGTTLDGFL
RAKVFVKRFV RAVLSEDSRA RVGVATYSRE LLVAVPVGEY QDVPDLVWSL DGIPFRGGPT
LTGSALRQAA ERGFGSATRT GQDRPRRVVV LLTESHSEDE VAGPARHARA RELLLLGVGS
EAVRAELEEI TGSPKHVMVY SDPQDLFNQI PELQGKLCSR QRPGCRTQAL DLVFMLDTSA
SVGPENFAQM QSFVRSCALQ FEVNPDVTQV GLVVYGSQVQ TAFGLDTKPT RAAMLRAISQ
APYLGGVGSA GTALLHIYDK VMTVQRGARP GVPKAVVVLT GGRGAEDAAV PAQKLRNNGI
SVLVVGVGPV LSEGLRRLAG PRDSLIHVAA YADLRYHQDV LIEWLCGGEW GNPHPQGCPH
GRPSA*
speed 1.65 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

Problems