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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000368373
Querying Taster for transcript #2: ENST00000327247
Querying Taster for transcript #3: ENST00000427500
Querying Taster for transcript #4: ENST00000536770
Querying Taster for transcript #5: ENST00000428024
MT speed 0 s - this script 4.497388 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GBAdisease_causing_automatic0.999731573646995simple_aaeaffected0A348Vsingle base exchangers78396650show file
GBAdisease_causing_automatic0.999731573646995simple_aaeaffected0A348Vsingle base exchangers78396650show file
GBAdisease_causing_automatic0.999731573646995simple_aaeaffected0A235Vsingle base exchangers78396650show file
GBAdisease_causing_automatic0.999800507292538simple_aaeaffected0A299Vsingle base exchangers78396650show file
GBAdisease_causing_automatic0.999800507292538simple_aaeaffected0A261Vsingle base exchangers78396650show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999731573646995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000368373
Genbank transcript ID NM_000157
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.1043C>T
cDNA.1165C>T
g.8437C>T
AA changes A348V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 348
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      348DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    348DPEAAKYVHGIVVHWYLDFLAPA
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330YVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  375SIDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  331DPTAAQYVHGIAIHWYEDFIDPA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
346352STRANDlost
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1611 / 1611
position (AA) of stopcodon in wt / mu AA sequence 537 / 537
position of stopcodon in wt / mu cDNA 1733 / 1733
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 123 / 123
chromosome 1
strand -1
last intron/exon boundary 1628
theoretical NMD boundary in CDS 1455
length of CDS 1611
coding sequence (CDS) position 1043
cDNA position
(for ins/del: last normal base / first normal base)		 1165
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIVVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
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: 0.999731573646995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000327247
Genbank transcript ID NM_001005741
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.1043C>T
cDNA.1276C>T
g.8437C>T
AA changes A348V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 348
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      348DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    348DPEAAKYVHGIVVHWYLDFLAPA
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330YVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  375SIDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  331DPTAAQYVHGIAIHWYEDFIDPA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
346352STRANDlost
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1611 / 1611
position (AA) of stopcodon in wt / mu AA sequence 537 / 537
position of stopcodon in wt / mu cDNA 1844 / 1844
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 234 / 234
chromosome 1
strand -1
last intron/exon boundary 1739
theoretical NMD boundary in CDS 1455
length of CDS 1611
coding sequence (CDS) position 1043
cDNA position
(for ins/del: last normal base / first normal base)		 1276
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIAVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGLLLTLQP EQKFQKVKGF
GGAMTDAAAL NILALSPPAQ NLLLKSYFSE EGIGYNIIRV PMASCDFSIR TYTYADTPDD
FQLHNFSLPE EDTKLKIPLI HRALQLAQRP VSLLASPWTS PTWLKTNGAV NGKGSLKGQP
GDIYHQTWAR YFVKFLDAYA EHKLQFWAVT AENEPSAGLL SGYPFQCLGF TPEHQRDFIA
RDLGPTLANS THHNVRLLML DDQRLLLPHW AKVVLTDPEA AKYVHGIVVH WYLDFLAPAK
ATLGETHRLF PNTMLFASEA CVGSKFWEQS VRLGSWDRGM QYSHSIITNL LYHVVGWTDW
NLALNPEGGP NWVRNFVDSP IIVDITKDTF YKQPMFYHLG HFSKFIPEGS QRVGLVASQK
NDLDAVALMH PDGSAVVVVL NRSSKDVPLT IKDPAVGFLE TISPGYSIHT YLWRRQ*
speed 1.38 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: 0.999731573646995 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000536770
Genbank transcript ID N/A
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.704C>T
cDNA.818C>T
g.8437C>T
AA changes A235V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 235
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      235DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    235DPEAAKYVHGIVVHWYL
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330DIKAARYVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  374RPNSIDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  331DPTAAQYVHGIAIHWYEDFIDPA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
235238STRANDlost
243261HELIXmight get lost (downstream of altered splice site)
267271STRANDmight get lost (downstream of altered splice site)
274274ACT_SITEProton donor.might get lost (downstream of altered splice site)
275279HELIXmight get lost (downstream of altered splice site)
284286STRANDmight get lost (downstream of altered splice site)
292301HELIXmight get lost (downstream of altered splice site)
303308HELIXmight get lost (downstream of altered splice site)
309309CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
311314TURNmight get lost (downstream of altered splice site)
315323STRANDmight get lost (downstream of altered splice site)
324326HELIXmight get lost (downstream of altered splice site)
329335HELIXmight get lost (downstream of altered splice site)
338341HELIXmight get lost (downstream of altered splice site)
346352STRANDmight get lost (downstream of altered splice site)
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 1386 / 1386
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 115 / 115
chromosome 1
strand -1
last intron/exon boundary 1281
theoretical NMD boundary in CDS 1116
length of CDS 1272
coding sequence (CDS) position 704
cDNA position
(for ins/del: last normal base / first normal base)		 818
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIAVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVRL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKDTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIVVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVRL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKDTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*
speed 0.95 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: 0.999800507292538 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000427500
Genbank transcript ID NM_001171812
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.896C>T
cDNA.1059C>T
g.8437C>T
AA changes A299V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 299
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      299DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    299DPEAAKYVHGIVVHWYLDFLAPA
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330YVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  374RPNSIDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  331DPTAAQYVHGIAIHWYEDFIDPA
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
292301HELIXlost
303308HELIXmight get lost (downstream of altered splice site)
309309CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
311314TURNmight get lost (downstream of altered splice site)
315323STRANDmight get lost (downstream of altered splice site)
324326HELIXmight get lost (downstream of altered splice site)
329335HELIXmight get lost (downstream of altered splice site)
338341HELIXmight get lost (downstream of altered splice site)
346352STRANDmight get lost (downstream of altered splice site)
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1464 / 1464
position (AA) of stopcodon in wt / mu AA sequence 488 / 488
position of stopcodon in wt / mu cDNA 1627 / 1627
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 164 / 164
chromosome 1
strand -1
last intron/exon boundary 1522
theoretical NMD boundary in CDS 1308
length of CDS 1464
coding sequence (CDS) position 896
cDNA position
(for ins/del: last normal base / first normal base)		 1059
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*
mutated AA sequence MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIVV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*
speed 0.92 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: 0.999800507292538 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910174)
  • known disease mutation: rs4316 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:155206217G>AN/A show variant in all transcripts   IGV
HGNC symbol GBA
Ensembl transcript ID ENST00000428024
Genbank transcript ID NM_001171811
UniProt peptide P04062
alteration type single base exchange
alteration region CDS
DNA changes c.782C>T
cDNA.1285C>T
g.8437C>T
AA changes A261V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 261
frameshift no
known variant Reference ID: rs78396650
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4316 (pathogenic for Gaucher's disease, type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910174)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0570.996
2.6631
(flanking)4.3460.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8446wt: 0.37 / mu: 0.59wt: TCATGGCATTGCTGTACATTGGTACCTGGACTTTCTGGCTC
mu: TCATGGCATTGTTGTACATTGGTACCTGGACTTTCTGGCTC		 attg|GTAC
Acc increased8442wt: 0.31 / mu: 0.42wt: ATGTTCATGGCATTGCTGTACATTGGTACCTGGACTTTCTG
mu: ATGTTCATGGCATTGTTGTACATTGGTACCTGGACTTTCTG		 gtac|ATTG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      261DPEAAKYVHGIAVHWYLDFLAPAK
mutated  not conserved    261DPEAAKYVHGIVVHWYLDFLAPA
Ptroglodytes  all identical  ENSPTRG00000001416  348DPEAAKYVHGIAVHWYLDFLAPA
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028048  327DPEAAKYVHGIAVHWYMDFLAPA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000010884  334DVHAGRYVHGVAVHWYMDSLVPA
Drerio  not conserved  ENSDARG00000076058  330DIKAARYVHGIGVHWYFDRLVPP
Dmelanogaster  all conserved  FBgn0051148  375IDYLDGLSLHWYWDEIF-G
Celegans  all identical  Y4C6B.6  330DPTAAQYVHGIAIH
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
243261HELIXlost
267271STRANDmight get lost (downstream of altered splice site)
274274ACT_SITEProton donor.might get lost (downstream of altered splice site)
275279HELIXmight get lost (downstream of altered splice site)
284286STRANDmight get lost (downstream of altered splice site)
292301HELIXmight get lost (downstream of altered splice site)
303308HELIXmight get lost (downstream of altered splice site)
309309CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
311314TURNmight get lost (downstream of altered splice site)
315323STRANDmight get lost (downstream of altered splice site)
324326HELIXmight get lost (downstream of altered splice site)
329335HELIXmight get lost (downstream of altered splice site)
338341HELIXmight get lost (downstream of altered splice site)
346352STRANDmight get lost (downstream of altered splice site)
354356HELIXmight get lost (downstream of altered splice site)
359369HELIXmight get lost (downstream of altered splice site)
373381STRANDmight get lost (downstream of altered splice site)
379379MUTAGENE->G: Decreases activity 1000-fold.might get lost (downstream of altered splice site)
379379ACT_SITENucleophile.might get lost (downstream of altered splice site)
386388STRANDmight get lost (downstream of altered splice site)
396411HELIXmight get lost (downstream of altered splice site)
414424STRANDmight get lost (downstream of altered splice site)
426428STRANDmight get lost (downstream of altered splice site)
440444STRANDmight get lost (downstream of altered splice site)
445447HELIXmight get lost (downstream of altered splice site)
449452STRANDmight get lost (downstream of altered splice site)
454463HELIXmight get lost (downstream of altered splice site)
470470CONFLICTS -> I (in Ref. 15; AA sequence).might get lost (downstream of altered splice site)
471479STRANDmight get lost (downstream of altered splice site)
482489STRANDmight get lost (downstream of altered splice site)
495501STRANDmight get lost (downstream of altered splice site)
501501CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
503505STRANDmight get lost (downstream of altered splice site)
507513STRANDmight get lost (downstream of altered splice site)
514516TURNmight get lost (downstream of altered splice site)
517523STRANDmight get lost (downstream of altered splice site)
527533STRANDmight get lost (downstream of altered splice site)
534534CONFLICTR -> H (in Ref. 1; AAA35873).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1350 / 1350
position (AA) of stopcodon in wt / mu AA sequence 450 / 450
position of stopcodon in wt / mu cDNA 1853 / 1853
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 504 / 504
chromosome 1
strand -1
last intron/exon boundary 1748
theoretical NMD boundary in CDS 1194
length of CDS 1350
coding sequence (CDS) position 782
cDNA position
(for ins/del: last normal base / first normal base)		 1285
gDNA position
(for ins/del: last normal base / first normal base)		 8437
chromosomal position
(for ins/del: last normal base / first normal base)		 155206217
original gDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered gDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
original cDNA sequence snippet TAAATATGTTCATGGCATTGCTGTACATTGGTACCTGGACT
altered cDNA sequence snippet TAAATATGTTCATGGCATTGTTGTACATTGGTACCTGGACT
wildtype AA sequence MELSMGPIQA NHTGTGLLLT LQPEQKFQKV KGFGGAMTDA AALNILALSP PAQNLLLKSY
FSEEGIGYNI IRVPMASCDF SIRTYTYADT PDDFQLHNFS LPEEDTKLKI PLIHRALQLA
QRPVSLLASP WTSPTWLKTN GAVNGKGSLK GQPGDIYHQT WARYFVKFLD AYAEHKLQFW
AVTAENEPSA GLLSGYPFQC LGFTPEHQRD FIARDLGPTL ANSTHHNVRL LMLDDQRLLL
PHWAKVVLTD PEAAKYVHGI AVHWYLDFLA PAKATLGETH RLFPNTMLFA SEACVGSKFW
EQSVRLGSWD RGMQYSHSII TNLLYHVVGW TDWNLALNPE GGPNWVRNFV DSPIIVDITK
DTFYKQPMFY HLGHFSKFIP EGSQRVGLVA SQKNDLDAVA LMHPDGSAVV VVLNRSSKDV
PLTIKDPAVG FLETISPGYS IHTYLWRRQ*
mutated AA sequence MELSMGPIQA NHTGTGLLLT LQPEQKFQKV KGFGGAMTDA AALNILALSP PAQNLLLKSY
FSEEGIGYNI IRVPMASCDF SIRTYTYADT PDDFQLHNFS LPEEDTKLKI PLIHRALQLA
QRPVSLLASP WTSPTWLKTN GAVNGKGSLK GQPGDIYHQT WARYFVKFLD AYAEHKLQFW
AVTAENEPSA GLLSGYPFQC LGFTPEHQRD FIARDLGPTL ANSTHHNVRL LMLDDQRLLL
PHWAKVVLTD PEAAKYVHGI VVHWYLDFLA PAKATLGETH RLFPNTMLFA SEACVGSKFW
EQSVRLGSWD RGMQYSHSII TNLLYHVVGW TDWNLALNPE GGPNWVRNFV DSPIIVDITK
DTFYKQPMFY HLGHFSKFIP EGSQRVGLVA SQKNDLDAVA LMHPDGSAVV VVLNRSSKDV
PLTIKDPAVG FLETISPGYS IHTYLWRRQ*
speed 0.92 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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