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: ENST00000442713
Querying Taster for transcript #2: ENST00000269445
MT speed 0 s - this script 4.36457 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DYMdisease_causing0.999995796027171simple_aaeaffectedE87Ksingle base exchangers120074164show file
DYMdisease_causing1without_aaeaffectedsingle base exchangers120074164show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999995796027171      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030532)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:46906063C>TN/A show variant in all transcripts   IGV
HGNC symbol DYM
Ensembl transcript ID ENST00000269445
Genbank transcript ID NM_017653
UniProt peptide Q7RTS9
alteration type single base exchange
alteration region CDS
DNA changes c.259G>A
cDNA.717G>A
g.81655G>A
AA changes E87K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
87
frameshift no
known variant Reference ID: rs120074164
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3661
4.321
(flanking)3.311
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased81646wt: 0.9424 / mu: 0.9493 (marginal change - not scored)wt: TAATTAAGGTCTTCCTTTCTAGAACCAAAGAACTAAAACTT
mu: TAATTAAGGTCTTCCTTTCTAGAACCAAAAAACTAAAACTT
 tcta|GAAC
Donor increased81657wt: 0.48 / mu: 0.68wt: AAAGAACTAAAACTT
mu: AAAAAACTAAAACTT
 AGAA|ctaa
Donor marginally increased81658wt: 0.4799 / mu: 0.5412 (marginal change - not scored)wt: AAGAACTAAAACTTT
mu: AAAAACTAAAACTTT
 GAAC|taaa
Donor increased81656wt: 0.20 / mu: 0.30wt: CAAAGAACTAAAACT
mu: CAAAAAACTAAAACT
 AAGA|acta
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      87ALIKVFLSRTKELKLSAECQNHIF
mutated  all conserved    87ALIKVFLSRTKKLKLSAECQNHI
Ptroglodytes  all identical  ENSPTRG00000010011  87ALIKVFLSRTKELKLSAECQNHI
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000012954  87XXXXXXXXXXXXXXXXXXXXXHI
Mmusculus  all identical  ENSMUSG00000035765  87ALTKVFLSRTRELRLSAECQNHI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000009986  87ALVKIFLARTKELKISTECQDQL
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0027607  88SLVTVFLEKTSELLSLSDQESNM
Celegans  all identical  C47D12.2  88AFIRLFLRRATELKTSEQCENKI
Xtropicalis  all identical  ENSXETG00000020310  88ALIRVFLSRTKELKISAECQNQL
protein features
start (aa)end (aa)featuredetails 
249249CONFLICTL -> P (in Ref. 2; BAC11088).might get lost (downstream of altered splice site)
381381CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
408408CONFLICTD -> Y (in Ref. 4; AAH64394).might get lost (downstream of altered splice site)
453453CONFLICTR -> K (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
458458MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
537537CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2010 / 2010
position (AA) of stopcodon in wt / mu AA sequence 670 / 670
position of stopcodon in wt / mu cDNA 2468 / 2468
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 459 / 459
chromosome 18
strand -1
last intron/exon boundary 2319
theoretical NMD boundary in CDS 1810
length of CDS 2010
coding sequence (CDS) position 259
cDNA position
(for ins/del: last normal base / first normal base)
717
gDNA position
(for ins/del: last normal base / first normal base)
81655
chromosomal position
(for ins/del: last normal base / first normal base)
46906063
original gDNA sequence snippet TCTTCCTTTCTAGAACCAAAGAACTAAAACTTTCAGCAGAA
altered gDNA sequence snippet TCTTCCTTTCTAGAACCAAAAAACTAAAACTTTCAGCAGAA
original cDNA sequence snippet TCTTCCTTTCTAGAACCAAAGAACTAAAACTTTCAGCAGAA
altered cDNA sequence snippet TCTTCCTTTCTAGAACCAAAAAACTAAAACTTTCAGCAGAA
wildtype AA sequence MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS
NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK
NITWYSERVL TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY
AAQRIISLFS LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN
SCLTNSLHHN PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD
IQLFTMDSD*
mutated AA sequence MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLVENNPR TGNLGALIKV FLSRTKKLKL SAECQNHIFI WQTHNALFII CCLLKVFICQ
MSEEELQLHF TYEEKSPGNY SSDSEDLLEE LLCCLMQLIT DIPLLDITYE ISVEAISTMV
VFLSCQLFHK EVLRQSISHK YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS
DGGGLLYGLA SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS
NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK
NITWYSERVL TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY
AAQRIISLFS LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN
SCLTNSLHHN PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD
IQLFTMDSD*
speed 1.54 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: without_aae, prob: 1      (explain)
Summary
  • known disease mutation at this position (HGMD CM030532)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:46906063C>TN/A show variant in all transcripts   IGV
HGNC symbol DYM
Ensembl transcript ID ENST00000442713
Genbank transcript ID N/A
UniProt peptide Q7RTS9
alteration type single base exchange
alteration region intron
DNA changes g.81655G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs120074164
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030532)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3661
4.321
(flanking)3.311
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased81646wt: 0.9424 / mu: 0.9493 (marginal change - not scored)wt: TAATTAAGGTCTTCCTTTCTAGAACCAAAGAACTAAAACTT
mu: TAATTAAGGTCTTCCTTTCTAGAACCAAAAAACTAAAACTT
 tcta|GAAC
Donor increased81657wt: 0.48 / mu: 0.68wt: AAAGAACTAAAACTT
mu: AAAAAACTAAAACTT
 AGAA|ctaa
Donor marginally increased81658wt: 0.4799 / mu: 0.5412 (marginal change - not scored)wt: AAGAACTAAAACTTT
mu: AAAAACTAAAACTTT
 GAAC|taaa
Donor increased81656wt: 0.20 / mu: 0.30wt: CAAAGAACTAAAACT
mu: CAAAAAACTAAAACT
 AAGA|acta
distance from splice site 11900
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
6666CONFLICTE -> K (in Ref. 2; BAC11088).might get lost (downstream of altered splice site)
249249CONFLICTL -> P (in Ref. 2; BAC11088).might get lost (downstream of altered splice site)
381381CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
408408CONFLICTD -> Y (in Ref. 4; AAH64394).might get lost (downstream of altered splice site)
453453CONFLICTR -> K (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
458458MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
537537CONFLICTE -> G (in Ref. 3; BAF83992).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 322 / 322
chromosome 18
strand -1
last intron/exon boundary 1612
theoretical NMD boundary in CDS 1240
length of CDS 1440
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
81655
chromosomal position
(for ins/del: last normal base / first normal base)
46906063
original gDNA sequence snippet TCTTCCTTTCTAGAACCAAAGAACTAAAACTTTCAGCAGAA
altered gDNA sequence snippet TCTTCCTTTCTAGAACCAAAAAACTAAAACTTTCAGCAGAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL KLLEEATISV
CRSLAGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA PNPYRQAIMS
FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL LLYTLLHQNS NIRTYMLART
DMENLVLPIL EILYHVEERN SHHVYMALII LLILTEDDGF NRSIHEVILK NITWYSERVL
TEISLGSLLI LVVIRTIQYN MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS
LLSKKHNKVL EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SCLTNSLHHN
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV ERVLEIIKQG
VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS AVGLYWNPQD IQLFTMDSD*
mutated AA sequence N/A
speed 0.88 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