Yum, tasty mutations...

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: ENST00000590230
Querying Taster for transcript #2: ENST00000263621
MT speed 0 s - this script 3.282152 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ELANEdisease_causing_automatic2.96720331468768e-10simple_aae0S126Lsingle base exchangers137854450show file
ELANEdisease_causing_automatic2.96720331468768e-10simple_aae0S126Lsingle base exchangers137854450show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 2.96720331468768e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002595)
  • known disease mutation at this position (HGMD CM097552)
  • known disease mutation at this position (HGMD CM144033)
  • known disease mutation: rs16745 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:855574C>TN/A show variant in all transcripts   IGV
HGNC symbol ELANE
Ensembl transcript ID ENST00000590230
Genbank transcript ID NM_001972
UniProt peptide P08246
alteration type single base exchange
alteration region CDS
DNA changes c.377C>T
cDNA.518C>T
g.4561C>T
AA changes S126L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 126
frameshift no
known variant Reference ID: rs137854450
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16745 (pathogenic for Cyclical neutropenia|Neutropenia, severe congenital 1, autosomal dominant|not specified) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4890.007
0.5670.012
(flanking)-0.8390.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      126LNDIVILQLNGSATINANVQVAQL
mutated  not conserved    126LQLNGLATINANVQVAQ
Ptroglodytes  all identical  ENSPTRG00000023440  106KGLNGSATINANVQVAQ
Mmulatta  all identical  ENSMMUG00000009674  126LQLNGSATINNNVRVAQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  125IQLNGSATINANVQVAQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000021647  122QNDIVILKLDRPVSLNGKVQ
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 945 / 945
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 142 / 142
chromosome 19
strand 1
last intron/exon boundary 739
theoretical NMD boundary in CDS 547
length of CDS 804
coding sequence (CDS) position 377
cDNA position
(for ins/del: last normal base / first normal base)		 518
gDNA position
(for ins/del: last normal base / first normal base)		 4561
chromosomal position
(for ins/del: last normal base / first normal base)		 855574
original gDNA sequence snippet ACCGCCACAGCTCAACGGGTCGGCCACCATCAACGCCAACG
altered gDNA sequence snippet ACCGCCACAGCTCAACGGGTTGGCCACCATCAACGCCAACG
original cDNA sequence snippet GATTCTCCAGCTCAACGGGTCGGCCACCATCAACGCCAACG
altered cDNA sequence snippet GATTCTCCAGCTCAACGGGTTGGCCACCATCAACGCCAACG
wildtype AA sequence MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
mutated AA sequence MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGLATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 1.09 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: 2.96720331468768e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002595)
  • known disease mutation at this position (HGMD CM097552)
  • known disease mutation at this position (HGMD CM144033)
  • known disease mutation: rs16745 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:855574C>TN/A show variant in all transcripts   IGV
HGNC symbol ELANE
Ensembl transcript ID ENST00000263621
Genbank transcript ID NM_001972
UniProt peptide P08246
alteration type single base exchange
alteration region CDS
DNA changes c.377C>T
cDNA.415C>T
g.4561C>T
AA changes S126L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 126
frameshift no
known variant Reference ID: rs137854450
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16745 (pathogenic for Cyclical neutropenia|Neutropenia, severe congenital 1, autosomal dominant|not specified) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
known disease mutation at this position, please check HGMD for details (HGMD ID CM144033)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002595)
known disease mutation at this position, please check HGMD for details (HGMD ID CM097552)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4890.007
0.5670.012
(flanking)-0.8390.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      126LNDIVILQLNGSATINANVQVAQL
mutated  not conserved    126LQLNGLATINANVQVAQ
Ptroglodytes  all identical  ENSPTRG00000023440  106KGLNGSATINANVQVAQ
Mmulatta  all identical  ENSMMUG00000009674  126LQLNGSATINNNVRVAQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  125IQLNGSATINANVQVAQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000021647  122QNDIVILKLDRPVSLNGKVQ
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 804 / 804
position (AA) of stopcodon in wt / mu AA sequence 268 / 268
position of stopcodon in wt / mu cDNA 842 / 842
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 39 / 39
chromosome 19
strand 1
last intron/exon boundary 636
theoretical NMD boundary in CDS 547
length of CDS 804
coding sequence (CDS) position 377
cDNA position
(for ins/del: last normal base / first normal base)		 415
gDNA position
(for ins/del: last normal base / first normal base)		 4561
chromosomal position
(for ins/del: last normal base / first normal base)		 855574
original gDNA sequence snippet ACCGCCACAGCTCAACGGGTCGGCCACCATCAACGCCAACG
altered gDNA sequence snippet ACCGCCACAGCTCAACGGGTTGGCCACCATCAACGCCAACG
original cDNA sequence snippet GATTCTCCAGCTCAACGGGTCGGCCACCATCAACGCCAACG
altered cDNA sequence snippet GATTCTCCAGCTCAACGGGTTGGCCACCATCAACGCCAACG
wildtype AA sequence MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
mutated AA sequence MTLGRRLACL FLACVLPALL LGGTALASEI VGGRRARPHA WPFMVSLQLR GGHFCGATLI
APNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGLATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 1.10 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