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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000388922
Querying Taster for transcript #2: ENST00000550683
Querying Taster for transcript #3: ENST00000419526
MT speed 0 s - this script 3.298834 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACVRL1disease_causing_automatic0.999999990197993simple_aaeaffected0I412Nsingle base exchangers121909286show file
ACVRL1disease_causing_automatic0.999999997835763simple_aaeaffected0I224Nsingle base exchangers121909286show file
ACVRL1disease_causing_automatic0.999999998391664simple_aaeaffected0I398Nsingle base exchangers121909286show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999990197993 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014973)
  • known disease mutation: rs8248 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52309964T>AN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000550683
Genbank transcript ID N/A
UniProt peptide P37023
alteration type single base exchange
alteration region CDS
DNA changes c.1235T>A
cDNA.1336T>A
g.9273T>A
AA changes I412N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 412
frameshift no
known variant Reference ID: rs121909286
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8248 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6181
4.8541
(flanking)4.0691
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained92680.70mu: TGGACTGACAACTGG GACT|gaca
distance from splice site 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      412TDCFESYKWTDIWAFGLVLWEIAR
mutated  not conserved    412TDCFESYKWTDNWAFGLVLW
Ptroglodytes  all identical  ENSPTRG00000004963  398TDCFESYKWTDIWAFGLVLWEIA
Mmulatta  all identical  ENSMMUG00000004982  405TDCFESYKWTDIWAFGLVLWEIA
Fcatus  all identical  ENSFCAG00000000265  400TDCFESYKWTDIWAFGLVLWEIA
Mmusculus  all identical  ENSMUSG00000000530  397TDCFESYKWTDIWAFGLVLWEIA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  365VFESYKQTDIWALGLVFWEIT
Drerio  all identical  ENSDARG00000018179  393ESYKQTDIWALGLVLWEIT
Dmelanogaster  all identical  FBgn0003317  460LECFEALRRTDIYAFGLVLWEVC
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000031897  368FESYKQTDLWAYGLVLWEIC
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
390410HELIXmight get lost (downstream of altered splice site)
424428TURNmight get lost (downstream of altered splice site)
435442HELIXmight get lost (downstream of altered splice site)
455459STRANDmight get lost (downstream of altered splice site)
460462TURNmight get lost (downstream of altered splice site)
463469HELIXmight get lost (downstream of altered splice site)
476478HELIXmight get lost (downstream of altered splice site)
482491HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1554 / 1554
position (AA) of stopcodon in wt / mu AA sequence 518 / 518
position of stopcodon in wt / mu cDNA 1655 / 1655
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 102 / 102
chromosome 12
strand 1
last intron/exon boundary 1521
theoretical NMD boundary in CDS 1369
length of CDS 1554
coding sequence (CDS) position 1235
cDNA position
(for ins/del: last normal base / first normal base)		 1336
gDNA position
(for ins/del: last normal base / first normal base)		 9273
chromosomal position
(for ins/del: last normal base / first normal base)		 52309964
original gDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered gDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
original cDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered cDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
wildtype AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGDPVKP SRGPLVTCTC ESPHCKGPTC
RGAWCTVVLV REEGRHPQEH RGCGNLHREL CRGRPTEFVN HYCCDSHLCN HNVSLVLEAT
QPPSEQPGTD GQLALILGPV LALLALVALG VLGLWHVRRR QEKQRGLHSE LGESSLILKA
SEQGDSMLGD LLDSDCTTGS GSGLPFLVQR TVARQVALVE CVGKGRYGEV WRGLWHGESV
AVKIFSSRDE QSWFRETEIY NTVLLRHDNI LGFIASDMTS RNSSTQLWLI THYHEHGSLY
DFLQRQTLEP HLALRLAVSA ACGLAHLHVE IFGTQGKPAI AHRDFKSRNV LVKSNLQCCI
ADLGLAVMHS QGSDYLDIGN NPRVGTKRYM APEVLDEQIR TDCFESYKWT DIWAFGLVLW
EIARRTIVNG IVEDYRPPFY DVVPNDPSFE DMKKVVCVDQ QTPTIPNRLA ADPVLSGLAQ
MMRECWYPNP SARLTALRIK KTLQKISNSP EKPKVIQ*
mutated AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGDPVKP SRGPLVTCTC ESPHCKGPTC
RGAWCTVVLV REEGRHPQEH RGCGNLHREL CRGRPTEFVN HYCCDSHLCN HNVSLVLEAT
QPPSEQPGTD GQLALILGPV LALLALVALG VLGLWHVRRR QEKQRGLHSE LGESSLILKA
SEQGDSMLGD LLDSDCTTGS GSGLPFLVQR TVARQVALVE CVGKGRYGEV WRGLWHGESV
AVKIFSSRDE QSWFRETEIY NTVLLRHDNI LGFIASDMTS RNSSTQLWLI THYHEHGSLY
DFLQRQTLEP HLALRLAVSA ACGLAHLHVE IFGTQGKPAI AHRDFKSRNV LVKSNLQCCI
ADLGLAVMHS QGSDYLDIGN NPRVGTKRYM APEVLDEQIR TDCFESYKWT DNWAFGLVLW
EIARRTIVNG IVEDYRPPFY DVVPNDPSFE DMKKVVCVDQ QTPTIPNRLA ADPVLSGLAQ
MMRECWYPNP SARLTALRIK KTLQKISNSP EKPKVIQ*
speed 0.30 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

disease causing

 Model: simple_aae, prob: 0.999999997835763 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014973)
  • known disease mutation: rs8248 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52309964T>AN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000419526
Genbank transcript ID N/A
UniProt peptide P37023
alteration type single base exchange
alteration region CDS
DNA changes c.671T>A
cDNA.733T>A
g.9273T>A
AA changes I224N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 224
frameshift no
known variant Reference ID: rs121909286
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8248 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6181
4.8541
(flanking)4.0691
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained92680.70mu: TGGACTGACAACTGG GACT|gaca
distance from splice site 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      224TDCFESYKWTDIWAFGLVLWEIAR
mutated  not conserved    224TDCFESYKWTDNWAFGLVLWEIA
Ptroglodytes  all identical  ENSPTRG00000004963  398CFESYKWTDIWAFGLVLWEIA
Mmulatta  all identical  ENSMMUG00000004982  405TDCFESYKWTDIWAFGLVLWEIA
Fcatus  all identical  ENSFCAG00000000265  400CFESYKWTDIWAFGLVLWEIA
Mmusculus  all identical  ENSMUSG00000000530  397CFESYKWTDIWAFGLVLWEIA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  365VFESYKQTDIWALGLVFWEIT
Drerio  all identical  ENSDARG00000018179  393VFESYKQTDIWALGLVLWEIT
Dmelanogaster  all identical  FBgn0003317  460CFEALRRTDIYAFGLVLWEVC
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000031897  368SFESYKQTDLWAYGLVLWEIC
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
224231STRANDlost
229229BINDINGATP (By similarity).might get lost (downstream of altered splice site)
233235HELIXmight get lost (downstream of altered splice site)
236248HELIXmight get lost (downstream of altered splice site)
259265STRANDmight get lost (downstream of altered splice site)
272278STRANDmight get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
296314HELIXmight get lost (downstream of altered splice site)
325327STRANDmight get lost (downstream of altered splice site)
330330ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
335338STRANDmight get lost (downstream of altered splice site)
344346STRANDmight get lost (downstream of altered splice site)
353355STRANDmight get lost (downstream of altered splice site)
357359STRANDmight get lost (downstream of altered splice site)
373375HELIXmight get lost (downstream of altered splice site)
378381HELIXmight get lost (downstream of altered splice site)
390410HELIXmight get lost (downstream of altered splice site)
424428TURNmight get lost (downstream of altered splice site)
435442HELIXmight get lost (downstream of altered splice site)
455459STRANDmight get lost (downstream of altered splice site)
460462TURNmight get lost (downstream of altered splice site)
463469HELIXmight get lost (downstream of altered splice site)
476478HELIXmight get lost (downstream of altered splice site)
482491HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1052 / 1052
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 63 / 63
chromosome 12
strand 1
last intron/exon boundary 918
theoretical NMD boundary in CDS 805
length of CDS 990
coding sequence (CDS) position 671
cDNA position
(for ins/del: last normal base / first normal base)		 733
gDNA position
(for ins/del: last normal base / first normal base)		 9273
chromosomal position
(for ins/del: last normal base / first normal base)		 52309964
original gDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered gDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
original cDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered cDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
wildtype AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKGRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YMAPEVLDEQ IRTDCFESYK WTDIWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*
mutated AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKGRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YMAPEVLDEQ IRTDCFESYK WTDNWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*
speed 0.97 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

disease causing

 Model: simple_aae, prob: 0.999999998391664 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014973)
  • known disease mutation: rs8248 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52309964T>AN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000388922
Genbank transcript ID NM_000020
UniProt peptide P37023
alteration type single base exchange
alteration region CDS
DNA changes c.1193T>A
cDNA.1476T>A
g.9273T>A
AA changes I398N Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 398
frameshift no
known variant Reference ID: rs121909286
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8248 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014973)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6181
4.8541
(flanking)4.0691
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained92680.70mu: TGGACTGACAACTGG GACT|gaca
distance from splice site 54
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      398TDCFESYKWTDIWAFGLVLWEIAR
mutated  not conserved    398TDCFESYKWTDNWAFGLVLWEIA
Ptroglodytes  all identical  ENSPTRG00000004963  398TDCFESYKWTDIWAFGLVLWEIA
Mmulatta  all identical  ENSMMUG00000004982  405TDCFESYKWTDIWAFGLVLWEIA
Fcatus  all identical  ENSFCAG00000000265  400TDCFESYKWTDIWAFGLVLWEIA
Mmusculus  all identical  ENSMUSG00000000530  397TDCFESYKWTDIWAFGLVLWEIA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  365VFESYKQTDIWALGLVFWEIT
Drerio  all identical  ENSDARG00000018179  393ESYKQTDIWALGLVLWEIT
Dmelanogaster  all identical  FBgn0003317  460LECFEALRRTDIYAFGLVLWEVC
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000031897  368FESYKQTDLWAYGLVLWEIC
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
390410HELIXlost
424428TURNmight get lost (downstream of altered splice site)
435442HELIXmight get lost (downstream of altered splice site)
455459STRANDmight get lost (downstream of altered splice site)
460462TURNmight get lost (downstream of altered splice site)
463469HELIXmight get lost (downstream of altered splice site)
476478HELIXmight get lost (downstream of altered splice site)
482491HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1512 / 1512
position (AA) of stopcodon in wt / mu AA sequence 504 / 504
position of stopcodon in wt / mu cDNA 1795 / 1795
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 284 / 284
chromosome 12
strand 1
last intron/exon boundary 1661
theoretical NMD boundary in CDS 1327
length of CDS 1512
coding sequence (CDS) position 1193
cDNA position
(for ins/del: last normal base / first normal base)		 1476
gDNA position
(for ins/del: last normal base / first normal base)		 9273
chromosomal position
(for ins/del: last normal base / first normal base)		 52309964
original gDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered gDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
original cDNA sequence snippet GTCCTACAAGTGGACTGACATCTGGGCCTTTGGCCTGGTGC
altered cDNA sequence snippet GTCCTACAAGTGGACTGACAACTGGGCCTTTGGCCTGGTGC
wildtype AA sequence MTLGSPRKGL LMLLMALVTQ GDPVKPSRGP LVTCTCESPH CKGPTCRGAW CTVVLVREEG
RHPQEHRGCG NLHRELCRGR PTEFVNHYCC DSHLCNHNVS LVLEATQPPS EQPGTDGQLA
LILGPVLALL ALVALGVLGL WHVRRRQEKQ RGLHSELGES SLILKASEQG DSMLGDLLDS
DCTTGSGSGL PFLVQRTVAR QVALVECVGK GRYGEVWRGL WHGESVAVKI FSSRDEQSWF
RETEIYNTVL LRHDNILGFI ASDMTSRNSS TQLWLITHYH EHGSLYDFLQ RQTLEPHLAL
RLAVSAACGL AHLHVEIFGT QGKPAIAHRD FKSRNVLVKS NLQCCIADLG LAVMHSQGSD
YLDIGNNPRV GTKRYMAPEV LDEQIRTDCF ESYKWTDIWA FGLVLWEIAR RTIVNGIVED
YRPPFYDVVP NDPSFEDMKK VVCVDQQTPT IPNRLAADPV LSGLAQMMRE CWYPNPSARL
TALRIKKTLQ KISNSPEKPK VIQ*
mutated AA sequence MTLGSPRKGL LMLLMALVTQ GDPVKPSRGP LVTCTCESPH CKGPTCRGAW CTVVLVREEG
RHPQEHRGCG NLHRELCRGR PTEFVNHYCC DSHLCNHNVS LVLEATQPPS EQPGTDGQLA
LILGPVLALL ALVALGVLGL WHVRRRQEKQ RGLHSELGES SLILKASEQG DSMLGDLLDS
DCTTGSGSGL PFLVQRTVAR QVALVECVGK GRYGEVWRGL WHGESVAVKI FSSRDEQSWF
RETEIYNTVL LRHDNILGFI ASDMTSRNSS TQLWLITHYH EHGSLYDFLQ RQTLEPHLAL
RLAVSAACGL AHLHVEIFGT QGKPAIAHRD FKSRNVLVKS NLQCCIADLG LAVMHSQGSD
YLDIGNNPRV GTKRYMAPEV LDEQIRTDCF ESYKWTDNWA FGLVLWEIAR RTIVNGIVED
YRPPFYDVVP NDPSFEDMKK VVCVDQQTPT IPNRLAADPV LSGLAQMMRE CWYPNPSARL
TALRIKKTLQ KISNSPEKPK VIQ*
speed 0.27 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

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