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 3.19 s - this script 8.113265 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ELANEdisease_causing_automatic0.998813708075947simple_aaeaffected0L206Fsingle base exchangers137854446show file
ELANEdisease_causing_automatic0.998813708075947simple_aaeaffected0L206Fsingle base exchangers137854446show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998813708075947 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993144)
  • known disease mutation: rs16739 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:855978G>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.618G>T
cDNA.759G>T
g.4965G>T
AA changes L206F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS
206
frameshift no
known variant Reference ID: rs137854446
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16739 (pathogenic for Cyclical neutropenia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7551
3.3081
(flanking)1.1431
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4969wt: 0.56 / mu: 0.96wt: ACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCACGGA
mu: ACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGA
 gtct|GCAA
Acc marginally increased4965wt: 0.3064 / mu: 0.3170 (marginal change - not scored)wt: GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
mu: GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
 cttg|GTCT
Acc increased4976wt: 0.25 / mu: 0.59wt: CAGCCCCTTGGTCTGCAACGGGCTAATCCACGGAATTGCCT
mu: CAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAATTGCCT
 acgg|GCTA
Acc increased4973wt: 0.21 / mu: 0.64wt: CGGCAGCCCCTTGGTCTGCAACGGGCTAATCCACGGAATTG
mu: CGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAATTG
 gcaa|CGGG
Donor marginally increased4969wt: 0.9864 / mu: 0.9927 (marginal change - not scored)wt: TGGTCTGCAACGGGC
mu: TTGTCTGCAACGGGC
 GTCT|gcaa
Acc gained49700.39mu: CTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAA tctg|CAAC
Acc gained49670.35mu: GGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACG ttgt|CTGC
Acc gained49710.55mu: TCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAAT ctgc|AACG
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      206AGVCFGDSGSPLVCNGLIHGIASF
mutated  not conserved    206AGVCFGDSGSPFVCNGLIHGIAS
Ptroglodytes  all identical  ENSPTRG00000023440  186AGVCFGDSGSPLVCNGLIHGIAS
Mmulatta  all identical  ENSMMUG00000009674  206AGVCFGDSGSPLVCNGLIHGIAS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  205AGICFGDSGGPLVCNNLVQGIDS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021647  203AGICFGDSGGPLVCNGVIQGITS
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
205208STRANDlost
208208DISULFIDmight get lost (downstream of altered splice site)
211222STRANDmight get lost (downstream of altered splice site)
223223DISULFIDmight get lost (downstream of altered splice site)
226228STRANDmight get lost (downstream of altered splice site)
230234STRANDmight get lost (downstream of altered splice site)
235238HELIXmight get lost (downstream of altered splice site)
239246HELIXmight get lost (downstream of altered splice site)
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 618
cDNA position
(for ins/del: last normal base / first normal base)
759
gDNA position
(for ins/del: last normal base / first normal base)
4965
chromosomal position
(for ins/del: last normal base / first normal base)
855978
original gDNA sequence snippet GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
altered gDNA sequence snippet GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
original cDNA sequence snippet GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
altered cDNA sequence snippet GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
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
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPFVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 1.71 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: 0.998813708075947 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993144)
  • known disease mutation: rs16739 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:855978G>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.618G>T
cDNA.656G>T
g.4965G>T
AA changes L206F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS
206
frameshift no
known variant Reference ID: rs137854446
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16739 (pathogenic for Cyclical neutropenia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993144)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7551
3.3081
(flanking)1.1431
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased4969wt: 0.56 / mu: 0.96wt: ACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCACGGA
mu: ACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGA
 gtct|GCAA
Acc marginally increased4965wt: 0.3064 / mu: 0.3170 (marginal change - not scored)wt: GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
mu: GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
 cttg|GTCT
Acc increased4976wt: 0.25 / mu: 0.59wt: CAGCCCCTTGGTCTGCAACGGGCTAATCCACGGAATTGCCT
mu: CAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAATTGCCT
 acgg|GCTA
Acc increased4973wt: 0.21 / mu: 0.64wt: CGGCAGCCCCTTGGTCTGCAACGGGCTAATCCACGGAATTG
mu: CGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAATTG
 gcaa|CGGG
Donor marginally increased4969wt: 0.9864 / mu: 0.9927 (marginal change - not scored)wt: TGGTCTGCAACGGGC
mu: TTGTCTGCAACGGGC
 GTCT|gcaa
Acc gained49700.39mu: CTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAA tctg|CAAC
Acc gained49670.35mu: GGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACG ttgt|CTGC
Acc gained49710.55mu: TCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCACGGAAT ctgc|AACG
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      206AGVCFGDSGSPLVCNGLIHGIASF
mutated  not conserved    206AGVCFGDSGSPFVCNGLIHGIAS
Ptroglodytes  all identical  ENSPTRG00000023440  186AGVCFGDSGSPLVCNGLIHGIAS
Mmulatta  all identical  ENSMMUG00000009674  206AGVCFGDSGSPLVCNGLIHGIAS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000020125  205AGICFGDSGGPLVCNNLVQGIDS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021647  203AGICFGDSGGPLVCNGVIQGITS
protein features
start (aa)end (aa)featuredetails 
30247DOMAINPeptidase S1.lost
205208STRANDlost
208208DISULFIDmight get lost (downstream of altered splice site)
211222STRANDmight get lost (downstream of altered splice site)
223223DISULFIDmight get lost (downstream of altered splice site)
226228STRANDmight get lost (downstream of altered splice site)
230234STRANDmight get lost (downstream of altered splice site)
235238HELIXmight get lost (downstream of altered splice site)
239246HELIXmight get lost (downstream of altered splice site)
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 618
cDNA position
(for ins/del: last normal base / first normal base)
656
gDNA position
(for ins/del: last normal base / first normal base)
4965
chromosomal position
(for ins/del: last normal base / first normal base)
855978
original gDNA sequence snippet GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
altered gDNA sequence snippet GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
original cDNA sequence snippet GGGGACTCCGGCAGCCCCTTGGTCTGCAACGGGCTAATCCA
altered cDNA sequence snippet GGGGACTCCGGCAGCCCCTTTGTCTGCAACGGGCTAATCCA
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
LQLNGSATIN ANVQVAQLPA QGRRLGNGVQ CLAMGWGLLG RNRGIASVLQ ELNVTVVTSL
CRRSNVCTLV RGRQAGVCFG DSGSPFVCNG LIHGIASFVR GGCASGLYPD AFAPVAQFVN
WIDSIIQRSE DNPCPHPRDP DPASRTH*
speed 1.48 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