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: ENST00000374580
Querying Taster for transcript #2: ENST00000374574
MT speed 2.82 s - this script 8.495977 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BMPR2disease_causing_automatic0.999999979748946simple_aae0R491Wsingle base exchangers137852746show file
BMPR2disease_causing_automatic0.999999979748946simple_aae0R491Wsingle base exchangers137852746show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999979748946 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002241)
  • known disease mutation: rs8802 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:203417496C>TN/A show variant in all transcripts   IGV
HGNC symbol BMPR2
Ensembl transcript ID ENST00000374580
Genbank transcript ID NM_001204
UniProt peptide Q13873
alteration type single base exchange
alteration region CDS
DNA changes c.1471C>T
cDNA.2010C>T
g.175838C>T
AA changes R491W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
491
frameshift no
known variant Reference ID: rs137852746
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8802 (pathogenic for Pulmonary arterial hypertension|Pulmonary Hypertension, Primary, 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4941
3.1721
(flanking)6.0961
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 increased175831wt: 0.3785 / mu: 0.3966 (marginal change - not scored)wt: GATGCAGAGGCTCGG
mu: GATGCAGAGGCTTGG
 TGCA|gagg
distance from splice site 58
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      491IEDCWDQDAEARLTAQCAEERMAE
mutated  not conserved    491EDCWDQDAEAWLTAQCAEERMA
Ptroglodytes  all identical  ENSPTRG00000029076  491EDCWDQDAEARLTAQCAEERMA
Mmulatta  all identical  ENSMMUG00000009009  493IEDCWDQDAEARLTAQCAEERMA
Fcatus  no alignment  ENSFCAG00000014094  n/a
Mmusculus  all identical  ENSMUSG00000067336  491EDCWDQDAEARLTAQCAEERMA
Ggallus  all identical  ENSGALG00000008459  484IEDCWDQDAEARLTAQCA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000020057  499ARLTAQCAEERMA
Dmelanogaster  all identical  FBgn0024179  516CEDCWDHDADARLTSLCAEERMQ
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000022074  502IDDCWDQDAEARLTAQCAEERMA
protein features
start (aa)end (aa)featuredetails 
1721038TOPO_DOMCytoplasmic (Potential).lost
203504DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3117 / 3117
position (AA) of stopcodon in wt / mu AA sequence 1039 / 1039
position of stopcodon in wt / mu cDNA 3656 / 3656
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 540 / 540
chromosome 2
strand 1
last intron/exon boundary 3406
theoretical NMD boundary in CDS 2816
length of CDS 3117
coding sequence (CDS) position 1471
cDNA position
(for ins/del: last normal base / first normal base)
2010
gDNA position
(for ins/del: last normal base / first normal base)
175838
chromosomal position
(for ins/del: last normal base / first normal base)
203417496
original gDNA sequence snippet GGGACCAGGATGCAGAGGCTCGGCTTACTGCACAGTGTGCT
altered gDNA sequence snippet GGGACCAGGATGCAGAGGCTTGGCTTACTGCACAGTGTGCT
original cDNA sequence snippet GGGACCAGGATGCAGAGGCTCGGCTTACTGCACAGTGTGCT
altered cDNA sequence snippet GGGACCAGGATGCAGAGGCTTGGCTTACTGCACAGTGTGCT
wildtype AA sequence MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCCST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA RLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERN LSHNRRVPKI
GPYPDYSSSS YIEDSIHHTD SIVKNISSEH SMSSTPLTIG EKNRNSINYE RQQAQARIPS
PETSVTSLST NTTTTNTTGL TPSTGMTTIS EMPYPDETNL HTTNVAQSIG PTPVCLQLTE
EDLETNKLDP KEVDKNLKES SDENLMEHSL KQFSGPDPLS STSSSLLYPL IKLAVEATGQ
QDFTQTANGQ ACLIPDVLPT QIYPLPKQQN LPKRPTSLPL NTKNSTKEPR LKFGSKHKSN
LKQVETGVAK MNTINAAEPH VVTVTMNGVA GRNHSVNSHA ATTQYANGTV LSGQTTNIVT
HRAQEMLQNQ FIGEDTRLNI NSSPDEHEPL LRREQQAGHD EGVLDRLVDR RERPLEGGRT
NSNNNNSNPC SEQDVLAQGV PSTAADPGPS KPRRAQRPNS LDLSATNVLD GSSIQIGEST
QDGKSGSGEK IKKRVKTPYS LKRWRPSTWV ISTESLDCEV NNNGSNRAVH SKSSTAVYLA
EGGTATTMVS KDIGMNCL*
mutated AA sequence MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCCST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA WLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERN LSHNRRVPKI
GPYPDYSSSS YIEDSIHHTD SIVKNISSEH SMSSTPLTIG EKNRNSINYE RQQAQARIPS
PETSVTSLST NTTTTNTTGL TPSTGMTTIS EMPYPDETNL HTTNVAQSIG PTPVCLQLTE
EDLETNKLDP KEVDKNLKES SDENLMEHSL KQFSGPDPLS STSSSLLYPL IKLAVEATGQ
QDFTQTANGQ ACLIPDVLPT QIYPLPKQQN LPKRPTSLPL NTKNSTKEPR LKFGSKHKSN
LKQVETGVAK MNTINAAEPH VVTVTMNGVA GRNHSVNSHA ATTQYANGTV LSGQTTNIVT
HRAQEMLQNQ FIGEDTRLNI NSSPDEHEPL LRREQQAGHD EGVLDRLVDR RERPLEGGRT
NSNNNNSNPC SEQDVLAQGV PSTAADPGPS KPRRAQRPNS LDLSATNVLD GSSIQIGEST
QDGKSGSGEK IKKRVKTPYS LKRWRPSTWV ISTESLDCEV NNNGSNRAVH SKSSTAVYLA
EGGTATTMVS KDIGMNCL*
speed 1.56 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: 0.999999979748946 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002241)
  • known disease mutation: rs8802 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:203417496C>TN/A show variant in all transcripts   IGV
HGNC symbol BMPR2
Ensembl transcript ID ENST00000374574
Genbank transcript ID N/A
UniProt peptide Q13873
alteration type single base exchange
alteration region CDS
DNA changes c.1471C>T
cDNA.1512C>T
g.175838C>T
AA changes R491W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
491
frameshift no
known variant Reference ID: rs137852746
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8802 (pathogenic for Pulmonary arterial hypertension|Pulmonary Hypertension, Primary, 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002241)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4941
3.1721
(flanking)6.0961
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 increased175831wt: 0.3785 / mu: 0.3966 (marginal change - not scored)wt: GATGCAGAGGCTCGG
mu: GATGCAGAGGCTTGG
 TGCA|gagg
distance from splice site 58
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      491IEDCWDQDAEARLTAQCAEERMAE
mutated  not conserved    491EDCWDQDAEAWLTAQCAEERMA
Ptroglodytes  all identical  ENSPTRG00000029076  491EDCWDQDAEARLTAQCAEERMA
Mmulatta  all identical  ENSMMUG00000009009  493IEDCWDQDAEARLTAQCAEERMA
Fcatus  no alignment  ENSFCAG00000014094  n/a
Mmusculus  all identical  ENSMUSG00000067336  491EDCWDQDAEARLTAQCAEERMA
Ggallus  all identical  ENSGALG00000008459  484IEDCWDQDAEARLTAQCA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000020057  499ARLTAQCAEERMA
Dmelanogaster  all identical  FBgn0024179  516CEDCWDHDADARLTSLCAEERMQ
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000022074  502IDDCWDQDAEARLTAQCAEERMA
protein features
start (aa)end (aa)featuredetails 
1721038TOPO_DOMCytoplasmic (Potential).lost
203504DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1593 / 1593
position (AA) of stopcodon in wt / mu AA sequence 531 / 531
position of stopcodon in wt / mu cDNA 1634 / 1634
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 42 / 42
chromosome 2
strand 1
last intron/exon boundary 1628
theoretical NMD boundary in CDS 1536
length of CDS 1593
coding sequence (CDS) position 1471
cDNA position
(for ins/del: last normal base / first normal base)
1512
gDNA position
(for ins/del: last normal base / first normal base)
175838
chromosomal position
(for ins/del: last normal base / first normal base)
203417496
original gDNA sequence snippet GGGACCAGGATGCAGAGGCTCGGCTTACTGCACAGTGTGCT
altered gDNA sequence snippet GGGACCAGGATGCAGAGGCTTGGCTTACTGCACAGTGTGCT
original cDNA sequence snippet GGGACCAGGATGCAGAGGCTCGGCTTACTGCACAGTGTGCT
altered cDNA sequence snippet GGGACCAGGATGCAGAGGCTTGGCTTACTGCACAGTGTGCT
wildtype AA sequence MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCCST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA RLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERR *
mutated AA sequence MTSSLQRPWR VPWLPWTILL VSTAAASQNQ ERLCAFKDPY QQDLGIGESR ISHENGTILC
SKGSTCYGLW EKSKGDINLV KQGCWSHIGD PQECHYEECV VTTTPPSIQN GTYRFCCCST
DLCNVNFTEN FPPPDTTPLS PPHSFNRDET IIIALASVSV LAVLIVALCF GYRMLTGDRK
QGLHSMNMME AAASEPSLDL DNLKLLELIG RGRYGAVYKG SLDERPVAVK VFSFANRQNF
INEKNIYRVP LMEHDNIARF IVGDERVTAD GRMEYLLVME YYPNGSLCKY LSLHTSDWVS
SCRLAHSVTR GLAYLHTELP RGDHYKPAIS HRDLNSRNVL VKNDGTCVIS DFGLSMRLTG
NRLVRPGEED NAAISEVGTI RYMAPEVLEG AVNLRDCESA LKQVDMYALG LIYWEIFMRC
TDLFPGESVP EYQMAFQTEV GNHPTFEDMQ VLVSREKQRP KFPEAWKENS LAVRSLKETI
EDCWDQDAEA WLTAQCAEER MAELMMIWER NKSVSPTVNP MSTAMQNERR *
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

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