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 3.77625 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACVRL1disease_causing_automatic0.999999993877565simple_aae0W50Csingle base exchangers121909285show file
ACVRL1disease_causing_automatic0.999999993877565simple_aae0W64Csingle base exchangers121909285show file
ACVRL1disease_causing_automatic1without_aae0single base exchangers121909285show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993877565 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050019)
  • known disease mutation at this position (HGMD CM970040)
  • known disease mutation: rs8246 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52306971G>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.150G>T
cDNA.433G>T
g.6280G>T
AA changes W50C Score: 215 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 50
frameshift no
known variant Reference ID: rs121909285
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8246 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3781
4.3781
(flanking)1.0591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased6281wt: 0.7956 / mu: 0.8500 (marginal change - not scored)wt: CCTGGTGCACAGTAG
mu: CCTGTTGCACAGTAG		 TGGT|gcac
distance from splice site 89
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50PHCKGPTCRGAWCTVVLVREEGRH
mutated  not conserved    50PHCKGPTCRGACCTVVLVREEG
Ptroglodytes  all identical  ENSPTRG00000004963  50PHCKGPTCRGAWCTVVLVREEG
Mmulatta  all identical  ENSMMUG00000004982  50PHCRGPTCQGAWCTVVLVREEG
Fcatus  all identical  ENSFCAG00000000265  50PTCRGSTCQGAWCIVVLVREE
Mmusculus  all identical  ENSMUSG00000000530  50PHCKRPFCQGSWCTVVLVREQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000012725  28GKGTCTNQTCRGHVCFYTWL-----
Drerio  not conserved  ENSDARG00000018179  60TNLCENNSCWGRICFYTSV-----
Dmelanogaster  not conserved  FBgn0003317  83PPCRDPYEFTHTCQNAIQCWKSRTRDADG
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000031897  19ASCSGETCVGRVCYVTESYASESE
protein features
start (aa)end (aa)featuredetails 
22118TOPO_DOMExtracellular (Potential).lost
4256STRANDlost
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 150
cDNA position
(for ins/del: last normal base / first normal base)		 433
gDNA position
(for ins/del: last normal base / first normal base)		 6280
chromosomal position
(for ins/del: last normal base / first normal base)		 52306971
original gDNA sequence snippet CCTACCTGCCGGGGGGCCTGGTGCACAGTAGTGCTGGTGCG
altered gDNA sequence snippet CCTACCTGCCGGGGGGCCTGTTGCACAGTAGTGCTGGTGCG
original cDNA sequence snippet CCTACCTGCCGGGGGGCCTGGTGCACAGTAGTGCTGGTGCG
altered cDNA sequence snippet CCTACCTGCCGGGGGGCCTGTTGCACAGTAGTGCTGGTGCG
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 CKGPTCRGAC 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*
speed 0.52 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

disease causing

 Model: simple_aae, prob: 0.999999993877565 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050019)
  • known disease mutation at this position (HGMD CM970040)
  • known disease mutation: rs8246 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52306971G>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.192G>T
cDNA.293G>T
g.6280G>T
AA changes W64C Score: 215 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 64
frameshift no
known variant Reference ID: rs121909285
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8246 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3781
4.3781
(flanking)1.0591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased6281wt: 0.7956 / mu: 0.8500 (marginal change - not scored)wt: CCTGGTGCACAGTAG
mu: CCTGTTGCACAGTAG		 TGGT|gcac
distance from splice site 89
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      64PHCKGPTCRGAWCTVVLVREEGRH
mutated  not conserved    64RGACCTVVLVREEGR
Ptroglodytes  all identical  ENSPTRG00000004963  50PHCKGPTCRGAWCTVVLVREEG
Mmulatta  all identical  ENSMMUG00000004982  50PHCRGPTCQGAWCTVVLVREEG
Fcatus  all identical  ENSFCAG00000000265  50PTCRGSTCQGAWCIVVLVREE
Mmusculus  all identical  ENSMUSG00000000530  50PHCKRPFCQGSWCTVVLVREQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000012725  28GKGTCTNQTCRGHVCFYTWL-----
Drerio  not conserved  ENSDARG00000018179  60TNLCENNSCWGRICFYTSV-----
Dmelanogaster  not conserved  FBgn0003317  83PPCRDPYEFTHTCQNAIQCWKSRTRDADG
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000031897  19ASCSGETCVGRVCYVTESYASESE
protein features
start (aa)end (aa)featuredetails 
22118TOPO_DOMExtracellular (Potential).lost
6468STRANDlost
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 192
cDNA position
(for ins/del: last normal base / first normal base)		 293
gDNA position
(for ins/del: last normal base / first normal base)		 6280
chromosomal position
(for ins/del: last normal base / first normal base)		 52306971
original gDNA sequence snippet CCTACCTGCCGGGGGGCCTGGTGCACAGTAGTGCTGGTGCG
altered gDNA sequence snippet CCTACCTGCCGGGGGGCCTGTTGCACAGTAGTGCTGGTGCG
original cDNA sequence snippet CCTACCTGCCGGGGGGCCTGGTGCACAGTAGTGCTGGTGCG
altered cDNA sequence snippet CCTACCTGCCGGGGGGCCTGTTGCACAGTAGTGCTGGTGCG
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
RGACCTVVLV 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*
speed 1.36 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM050019)
  • known disease mutation at this position (HGMD CM970040)
  • known disease mutation: rs8246 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52306971G>TN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000419526
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.6280G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121909285
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8246 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970040)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3781
4.3781
(flanking)1.0591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased6281wt: 0.7956 / mu: 0.8500 (marginal change - not scored)wt: CCTGGTGCACAGTAG
mu: CCTGTTGCACAGTAG		 TGGT|gcac
distance from splice site 652
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 6280
chromosomal position
(for ins/del: last normal base / first normal base)		 52306971
original gDNA sequence snippet CCTACCTGCCGGGGGGCCTGGTGCACAGTAGTGCTGGTGCG
altered gDNA sequence snippet CCTACCTGCCGGGGGGCCTGTTGCACAGTAGTGCTGGTGCG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.39 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