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: ENST00000372037
Querying Taster for transcript #2: ENST00000224764
MT speed 2.92 s - this script 7.995651 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BMPR1Adisease_causing_automatic0.99999999999996simple_aaeaffected0C124Rsingle base exchangers199476087show file
BMPR1Adisease_causing_automatic0.99999999999996simple_aaeaffected0C124Rsingle base exchangers199476087show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999996 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014515)
  • known disease mutation: rs8234 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:88659587T>CN/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.370T>C
cDNA.915T>C
g.143192T>C
AA changes C124R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS
124
frameshift no
known variant Reference ID: rs199476087
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8234 (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 CM014515)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014515)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014515)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.541
3.8861
(flanking)4.6871
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 increased143190wt: 0.2021 / mu: 0.2032 (marginal change - not scored)wt: AATAGAATGTTGTCG
mu: AATAGAACGTTGTCG
 TAGA|atgt
Donor increased143187wt: 0.28 / mu: 0.62wt: GACAATAGAATGTTG
mu: GACAATAGAACGTTG
 CAAT|agaa
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      124SPKAQLRRTIECCRTNLCNQYLQP
mutated  not conserved    124TIERCRTNLCNQYLQ
Ptroglodytes  all identical  ENSPTRG00000002706  124TIECCRTNLCNQYLQ
Mmulatta  all identical  ENSMMUG00000011852  124TIECCRTNLCNQYLQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021796  124TIECCRTNLCNQYLQ
Ggallus  all identical  ENSGALG00000002003  124TIECCRTDFCNQDLQ
Trubripes  all identical  ENSTRUG00000011026  118RRTIECCNTDFCNRDLQ
Drerio  all identical  ENSDARG00000019728  124ECCQFDFCNQDLK
Dmelanogaster  all identical  FBgn0003716  148AAVPHLHGKNIVCCDKEDFC
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000003655  129ATLKSSSMLGETDFCNRDLQ
protein features
start (aa)end (aa)featuredetails 
24152TOPO_DOMExtracellular (Potential).lost
120125STRANDlost
124124DISULFIDlost
125125DISULFIDmight get lost (downstream of altered splice site)
130130DISULFIDmight get lost (downstream of altered splice site)
130133HELIXmight get lost (downstream of altered splice site)
153176TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
177532TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
204233DOMAINGS.might get lost (downstream of altered splice site)
215215MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
216216MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
218218MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
220220MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
234525DOMAINProtein kinase.might get lost (downstream of altered splice site)
240248NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
261261BINDINGATP (By similarity).might get lost (downstream of altered splice site)
362362ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
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 370
cDNA position
(for ins/del: last normal base / first normal base)
915
gDNA position
(for ins/del: last normal base / first normal base)
143192
chromosomal position
(for ins/del: last normal base / first normal base)
88659587
original gDNA sequence snippet AGCTACGCCGGACAATAGAATGTTGTCGGACCAATTTATGT
altered gDNA sequence snippet AGCTACGCCGGACAATAGAACGTTGTCGGACCAATTTATGT
original cDNA sequence snippet AGCTACGCCGGACAATAGAATGTTGTCGGACCAATTTATGT
altered cDNA sequence snippet AGCTACGCCGGACAATAGAACGTTGTCGGACCAATTTATGT
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
TIERCRTNLC 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*
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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999996 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM014515)
  • known disease mutation: rs8234 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:88659587T>CN/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.370T>C
cDNA.918T>C
g.143192T>C
AA changes C124R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS
124
frameshift no
known variant Reference ID: rs199476087
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs8234 (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 CM014515)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014515)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014515)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Rad21, Transcription Factor, Rad21 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.541
3.8861
(flanking)4.6871
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 increased143190wt: 0.2021 / mu: 0.2032 (marginal change - not scored)wt: AATAGAATGTTGTCG
mu: AATAGAACGTTGTCG
 TAGA|atgt
Donor increased143187wt: 0.28 / mu: 0.62wt: GACAATAGAATGTTG
mu: GACAATAGAACGTTG
 CAAT|agaa
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      124SPKAQLRRTIECCRTNLCNQYLQP
mutated  not conserved    124TIERCRTNLCNQYLQ
Ptroglodytes  all identical  ENSPTRG00000002706  124TIECCRTNLCNQYLQ
Mmulatta  all identical  ENSMMUG00000011852  124TIECCRTNLCNQYLQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021796  124TIECCRTNLCNQYLQ
Ggallus  all identical  ENSGALG00000002003  124TIECCRTDFCNQDLQ
Trubripes  all identical  ENSTRUG00000011026  118RRTIECCNTDFCNRDLQ
Drerio  all identical  ENSDARG00000019728  124ECCQFDFCNQDLK
Dmelanogaster  all identical  FBgn0003716  148AAVPHLHGKNIVCCDKEDFC
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000003655  129ATLKSSSMLGETDFCNRDLQ
protein features
start (aa)end (aa)featuredetails 
24152TOPO_DOMExtracellular (Potential).lost
120125STRANDlost
124124DISULFIDlost
125125DISULFIDmight get lost (downstream of altered splice site)
130130DISULFIDmight get lost (downstream of altered splice site)
130133HELIXmight get lost (downstream of altered splice site)
153176TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
177532TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
204233DOMAINGS.might get lost (downstream of altered splice site)
215215MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
216216MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
218218MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
220220MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
234525DOMAINProtein kinase.might get lost (downstream of altered splice site)
240248NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
261261BINDINGATP (By similarity).might get lost (downstream of altered splice site)
362362ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
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 370
cDNA position
(for ins/del: last normal base / first normal base)
918
gDNA position
(for ins/del: last normal base / first normal base)
143192
chromosomal position
(for ins/del: last normal base / first normal base)
88659587
original gDNA sequence snippet AGCTACGCCGGACAATAGAATGTTGTCGGACCAATTTATGT
altered gDNA sequence snippet AGCTACGCCGGACAATAGAACGTTGTCGGACCAATTTATGT
original cDNA sequence snippet AGCTACGCCGGACAATAGAATGTTGTCGGACCAATTTATGT
altered cDNA sequence snippet AGCTACGCCGGACAATAGAACGTTGTCGGACCAATTTATGT
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
TIERCRTNLC 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*
speed 1.27 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

Problems