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 3.452737 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ELANEdisease_causing_automatic3.49838978409838e-06simple_aae0A61Vsingle base exchangers137854447show file
ELANEdisease_causing_automatic3.49838978409838e-06simple_aae0A61Vsingle base exchangers137854447show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 3.49838978409838e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993143)
  • known disease mutation: rs16740 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:852990C>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.182C>T
cDNA.323C>T
g.1977C>T
AA changes A61V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 61
frameshift no
known variant Reference ID: rs137854447
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16740 (pathogenic for Cyclical neutropenia|Neutropenia, severe congenital 1, autosomal dominant) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4030.129
1.4740.12
(flanking)-0.1970.032
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 increased1982wt: 0.2623 / mu: 0.2957 (marginal change - not scored)wt: CGCCCAACTTCGTCA
mu: TGCCCAACTTCGTCA		 CCCA|actt
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      61RGGHFCGATLIAPNFVMSAAHCVA
mutated  not conserved    61VPNFVMSAAHCV
Ptroglodytes  all identical  ENSPTRG00000023440  61APNFVMSAAHCV
Mmulatta  all identical  ENSMMUG00000009674  61APNFVMSAAHCV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  60ARNFVMSAAHCV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021647  57RGRHFCGGSLIAPQFLMTAAHCM
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
5261STRANDlost
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 182
cDNA position
(for ins/del: last normal base / first normal base)		 323
gDNA position
(for ins/del: last normal base / first normal base)		 1977
chromosomal position
(for ins/del: last normal base / first normal base)		 852990
original gDNA sequence snippet CTGCGGCGCCACCCTGATTGCGCCCAACTTCGTCATGTCGG
altered gDNA sequence snippet CTGCGGCGCCACCCTGATTGTGCCCAACTTCGTCATGTCGG
original cDNA sequence snippet CTGCGGCGCCACCCTGATTGCGCCCAACTTCGTCATGTCGG
altered cDNA sequence snippet CTGCGGCGCCACCCTGATTGTGCCCAACTTCGTCATGTCGG
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
VPNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 0.89 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: 3.49838978409838e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993143)
  • known disease mutation: rs16740 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:852990C>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.182C>T
cDNA.220C>T
g.1977C>T
AA changes A61V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 61
frameshift no
known variant Reference ID: rs137854447
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16740 (pathogenic for Cyclical neutropenia|Neutropenia, severe congenital 1, autosomal dominant) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993143)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4030.129
1.4740.12
(flanking)-0.1970.032
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 increased1982wt: 0.2623 / mu: 0.2957 (marginal change - not scored)wt: CGCCCAACTTCGTCA
mu: TGCCCAACTTCGTCA		 CCCA|actt
distance from splice site 43
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      61RGGHFCGATLIAPNFVMSAAHCVA
mutated  not conserved    61VPNFVMSAAHCV
Ptroglodytes  all identical  ENSPTRG00000023440  61APNFVMSAAHCV
Mmulatta  all identical  ENSMMUG00000009674  61APNFVMSAAHCV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  60ARNFVMSAAHCV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021647  57RGRHFCGGSLIAPQFLMTAAHCM
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
5261STRANDlost
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 182
cDNA position
(for ins/del: last normal base / first normal base)		 220
gDNA position
(for ins/del: last normal base / first normal base)		 1977
chromosomal position
(for ins/del: last normal base / first normal base)		 852990
original gDNA sequence snippet CTGCGGCGCCACCCTGATTGCGCCCAACTTCGTCATGTCGG
altered gDNA sequence snippet CTGCGGCGCCACCCTGATTGTGCCCAACTTCGTCATGTCGG
original cDNA sequence snippet CTGCGGCGCCACCCTGATTGCGCCCAACTTCGTCATGTCGG
altered cDNA sequence snippet CTGCGGCGCCACCCTGATTGTGCCCAACTTCGTCATGTCGG
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
VPNFVMSAAH CVANVNVRAV RVVLGAHNLS RREPTRQVFA VQRIFENGYD PVNLLNDIVI
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPLVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 0.62 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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