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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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000372037
Querying Taster for transcript #2: ENST00000224764
MT speed 2.68 s - this script 5.802089 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BMPR1Adisease_causing0.999999998645429simple_aaeA338Dsingle base exchangers199476086show file
BMPR1Adisease_causing0.999999998645429simple_aaeA338Dsingle base exchangers199476086show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998645429      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs8233 (probable pathogenic)
  • known disease mutation at this position (HGMD CM014517)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:88679073C>AN/A show variant in all transcripts   IGV
HGNC symbol BMPR1A
Ensembl transcript ID ENST00000372037
Genbank transcript ID N/A
UniProt peptide P36894
alteration type single base exchange
alteration region CDS
DNA changes c.1013C>A
cDNA.1558C>A
g.162678C>A
AA changes A338D Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS
338
frameshift no
known variant Reference ID: rs199476086
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs8233 (probable pathogenic for Generalized juvenile polyposis/juvenile polyposis coli|Hereditary cancer-predisposing syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.050.996
5.8521
(flanking)0.2941
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 increased162675wt: 0.6134 / mu: 0.6234 (marginal change - not scored)wt: CCTGCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCC
mu: CCTGCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCC
 attc|AGCT
distance from splice site 145
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      338DTRALLKLAYSAACGLCHLHTEIY
mutated  not conserved    338DTRALLKLAYSDACGLCHLHTEI
Ptroglodytes  all identical  ENSPTRG00000002706  338DTRALLKLAYSAACGLCHLHTEI
Mmulatta  all identical  ENSMMUG00000011852  338DTRALLKLAYSAACGLCHLHTEI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021796  338DTRALLKLAYSAACGLCHLHTEI
Ggallus  all identical  ENSGALG00000002003  339DNRALLKLAYSAACGLCHLHTEI
Trubripes  all identical  ENSTRUG00000011026  331DTQMLLRLAYSAACGLCHLHTEI
Drerio  all identical  ENSDARG00000019728  333DTQALLRLAFSAACGLCHLHTEI
Dmelanogaster  not conserved  FBgn0003716  370NPQKLQLLAFSLASGLAHLHDEI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003655  343DTRSLLKLAYSAACGLCHLHTEI
protein features
start (aa)end (aa)featuredetails 
177532TOPO_DOMCytoplasmic (Potential).lost
234525DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1599 / 1599
position (AA) of stopcodon in wt / mu AA sequence 533 / 533
position of stopcodon in wt / mu cDNA 2144 / 2144
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 546 / 546
chromosome 10
strand 1
last intron/exon boundary 2019
theoretical NMD boundary in CDS 1423
length of CDS 1599
coding sequence (CDS) position 1013
cDNA position
(for ins/del: last normal base / first normal base)
1558
gDNA position
(for ins/del: last normal base / first normal base)
162678
chromosomal position
(for ins/del: last normal base / first normal base)
88679073
original gDNA sequence snippet GCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCCACC
altered gDNA sequence snippet GCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCCACC
original cDNA sequence snippet GCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCCACC
altered cDNA sequence snippet GCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCCACC
wildtype AA sequence MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSAAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSCCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*
mutated AA sequence MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSDAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSCCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*
speed 1.42 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: 0.999999998645429      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs8233 (probable pathogenic)
  • known disease mutation at this position (HGMD CM014517)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:88679073C>AN/A show variant in all transcripts   IGV
HGNC symbol BMPR1A
Ensembl transcript ID ENST00000224764
Genbank transcript ID NM_004329
UniProt peptide P36894
alteration type single base exchange
alteration region CDS
DNA changes c.1013C>A
cDNA.1561C>A
g.162678C>A
AA changes A338D Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS
338
frameshift no
known variant Reference ID: rs199476086
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs8233 (probable pathogenic for Generalized juvenile polyposis/juvenile polyposis coli|Hereditary cancer-predisposing syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014517)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.050.996
5.8521
(flanking)0.2941
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 increased162675wt: 0.6134 / mu: 0.6234 (marginal change - not scored)wt: CCTGCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCC
mu: CCTGCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCC
 attc|AGCT
distance from splice site 145
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      338DTRALLKLAYSAACGLCHLHTEIY
mutated  not conserved    338DTRALLKLAYSDACGLCHLHTEI
Ptroglodytes  all identical  ENSPTRG00000002706  338DTRALLKLAYSAACGLCHLHTEI
Mmulatta  all identical  ENSMMUG00000011852  338DTRALLKLAYSAACGLCHLHTEI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021796  338DTRALLKLAYSAACGLCHLHTEI
Ggallus  all identical  ENSGALG00000002003  339DNRALLKLAYSAACGLCHLHTEI
Trubripes  all identical  ENSTRUG00000011026  331DTQMLLRLAYSAACGLCHLHTEI
Drerio  all identical  ENSDARG00000019728  333DTQALLRLAFSAACGLCHLHTEI
Dmelanogaster  not conserved  FBgn0003716  370NPQKLQLLAFSLASGLAHLHDEI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000003655  343DTRSLLKLAYSAACGLCHLHTEI
protein features
start (aa)end (aa)featuredetails 
177532TOPO_DOMCytoplasmic (Potential).lost
234525DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1599 / 1599
position (AA) of stopcodon in wt / mu AA sequence 533 / 533
position of stopcodon in wt / mu cDNA 2147 / 2147
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 549 / 549
chromosome 10
strand 1
last intron/exon boundary 2022
theoretical NMD boundary in CDS 1423
length of CDS 1599
coding sequence (CDS) position 1013
cDNA position
(for ins/del: last normal base / first normal base)
1561
gDNA position
(for ins/del: last normal base / first normal base)
162678
chromosomal position
(for ins/del: last normal base / first normal base)
88679073
original gDNA sequence snippet GCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCCACC
altered gDNA sequence snippet GCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCCACC
original cDNA sequence snippet GCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCCACC
altered cDNA sequence snippet GCTTAAATTGGCTTATTCAGATGCCTGTGGTCTGTGCCACC
wildtype AA sequence MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSAAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSCCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*
mutated AA sequence MPQLYIYIRL LGAYLFIISR VQGQNLDSML HGTGMKSDSD QKKSENGVTL APEDTLPFLK
CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR
TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IRWLVLLISM AVCIIAMIIF SSCFCYKHYC
KSISSRRRYN RDLEQDEAFI PVGESLKDLI DQSQSSGSGS GLPLLVQRTI AKQIQMVRQV
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDF LKCATLDTRA LLKLAYSDAC GLCHLHTEIY GTQGKPAIAH
RDLKSKNILI KKNGSCCIAD LGLAVKFNSD TNEVDVPLNT RVGTKRYMAP EVLDESLNKN
HFQPYIMADI YSFGLIIWEM ARRCITGGIV EEYQLPYYNM VPSDPSYEDM REVVCVKRLR
PIVSNRWNSD ECLRAVLKLM SECWAHNPAS RLTALRIKKT LAKMVESQDV KI*
speed 1.26 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