Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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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 3.586251 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACVRL1disease_causing_automatic0.999999959552613simple_aae0R411Wsingle base exchangers121909287show file
ACVRL1disease_causing_automatic0.999999991997937simple_aae0R425Wsingle base exchangers121909287show file
ACVRL1disease_causing_automatic0.999999993363299simple_aae0R237Wsingle base exchangers121909287show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999959552613 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012327)
  • known disease mutation: rs8251 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52310002C>TN/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.1231C>T
cDNA.1514C>T
g.9311C>T
AA changes R411W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 411
frameshift no
known variant Reference ID: rs121909287
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8251 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2|Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5920.781
1.8420.989
(flanking)5.811
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      411AFGLVLWEIARRTIVNGIVEDYRP
mutated  not conserved    411AFGLVLWEIARWTIVNGIVED
Ptroglodytes  all identical  ENSPTRG00000004963  411AFGLVLWEIARRTIVNGIVED
Mmulatta  all identical  ENSMMUG00000004982  418AFGLVLWEIARRTI
Fcatus  all identical  ENSFCAG00000000265  413AFGLVLWEIARRTIVNGIV
Mmusculus  all identical  ENSMUSG00000000530  410AFGLVLWEIARRTIINGIVE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  378ALGLVFWEITRRTIVNGIVEEYR
Drerio  all identical  ENSDARG00000018179  406ALGLVLWEITRRTIVNGIVEEYR
Dmelanogaster  all identical  FBgn0003317  473AFGLVLWEVCRRTISCGI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031897  381AYGLVLWEICRRTVVNGMVEDYR
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
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 1231
cDNA position
(for ins/del: last normal base / first normal base)		 1514
gDNA position
(for ins/del: last normal base / first normal base)		 9311
chromosomal position
(for ins/del: last normal base / first normal base)		 52310002
original gDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGTGAG
altered gDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGTGAG
original cDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGCATC
altered cDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGCATC
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 ESYKWTDIWA FGLVLWEIAR WTIVNGIVED
YRPPFYDVVP NDPSFEDMKK VVCVDQQTPT IPNRLAADPV LSGLAQMMRE CWYPNPSARL
TALRIKKTLQ KISNSPEKPK VIQ*
speed 0.76 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: 0.999999991997937 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012327)
  • known disease mutation: rs8251 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52310002C>TN/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.1273C>T
cDNA.1374C>T
g.9311C>T
AA changes R425W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 425
frameshift no
known variant Reference ID: rs121909287
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8251 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2|Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5920.781
1.8420.989
(flanking)5.811
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      425AFGLVLWEIARRTIVNGIVEDYRP
mutated  not conserved    425EIARWTIVNGIVEDYR
Ptroglodytes  all identical  ENSPTRG00000004963  411AFGLVLWEIARRTIVNGIVED
Mmulatta  all identical  ENSMMUG00000004982  418AFGLVLWEIARRTI
Fcatus  all identical  ENSFCAG00000000265  413AFGLVLWEIARRTIVNGIV
Mmusculus  all identical  ENSMUSG00000000530  410AFGLVLWEIARRTIINGIVE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  378ALGLVFWEITRRTIVNGIVEEYR
Drerio  all identical  ENSDARG00000018179  406ALGLVLWEITRRTIVNGIVEEYR
Dmelanogaster  all identical  FBgn0003317  473AFGLVLWEVCRRTISCGI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031897  381AYGLVLWEICRRTVVNGMVEDYR
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
424428TURNlost
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 1273
cDNA position
(for ins/del: last normal base / first normal base)		 1374
gDNA position
(for ins/del: last normal base / first normal base)		 9311
chromosomal position
(for ins/del: last normal base / first normal base)		 52310002
original gDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGTGAG
altered gDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGTGAG
original cDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGCATC
altered cDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGCATC
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 DIWAFGLVLW
EIARWTIVNG IVEDYRPPFY DVVPNDPSFE DMKKVVCVDQ QTPTIPNRLA ADPVLSGLAQ
MMRECWYPNP SARLTALRIK KTLQKISNSP EKPKVIQ*
speed 0.77 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: 0.999999993363299 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012327)
  • known disease mutation: rs8251 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52310002C>TN/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.709C>T
cDNA.771C>T
g.9311C>T
AA changes R237W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 237
frameshift no
known variant Reference ID: rs121909287
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8251 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2|Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012327)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5920.781
1.8420.989
(flanking)5.811
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      237AFGLVLWEIARRTIVNGIVEDYRP
mutated  not conserved    237AFGLVLWEIARWTIV
Ptroglodytes  all identical  ENSPTRG00000004963  411AFGLVLWEIARRTIVNGIVEDYR
Mmulatta  all identical  ENSMMUG00000004982  418AFGLVLWEIARRTIVNGIVEDYR
Fcatus  all identical  ENSFCAG00000000265  413AFGLVLWEIARRTIVNGIVEDYR
Mmusculus  all identical  ENSMUSG00000000530  410AFGLVLWEIARRTIINGIVEDYR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  378ALGLVFWEITRRTIVNGIVEEYR
Drerio  all identical  ENSDARG00000018179  406ALGLVLWEITRRTIVNGIVEEYR
Dmelanogaster  all identical  FBgn0003317  473AFGLVLWEVCRRTISCGIAEEYK
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031897  381AYGLVLWEICRRTVVNGMVEDYR
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
236248HELIXlost
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 709
cDNA position
(for ins/del: last normal base / first normal base)		 771
gDNA position
(for ins/del: last normal base / first normal base)		 9311
chromosomal position
(for ins/del: last normal base / first normal base)		 52310002
original gDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGTGAG
altered gDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGTGAG
original cDNA sequence snippet TGCTGTGGGAGATTGCCCGCCGGACCATCGTGAATGGCATC
altered cDNA sequence snippet TGCTGTGGGAGATTGCCCGCTGGACCATCGTGAATGGCATC
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 WTDIWAFGLV LWEIARWTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*
speed 0.65 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

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