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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000311916
Querying Taster for transcript #2: ENST00000370228
MT speed 1.96 s - this script 3.953216 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
TWNKdisease_causing_automatic0.999998173552585simple_aae0T457Isingle base exchangers80356544show file
TWNKdisease_causing_automatic0.999998173552585simple_aae0T457Isingle base exchangers80356544show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999998173552585 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM076376)
  • known disease mutation: rs4626 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:102749527C>TN/A show variant in all transcripts   IGV
HGNC symbol TWNK
Ensembl transcript ID ENST00000311916
Genbank transcript ID NM_001163813
UniProt peptide Q96RR1
alteration type single base exchange
alteration region CDS
DNA changes c.1370C>T
cDNA.1555C>T
g.2404C>T
AA changes T457I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 457
frameshift no
known variant Reference ID: rs80356544
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs4626 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral|Infantile onset spinocerebellar ataxia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)

known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)
known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9911
6.0431
(flanking)-0.6580.849
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 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      457ISNVRLARVMLTQFAEGRLEDQLD
mutated  not conserved    457ISNVRLARVMLIQFAEGRLEDQL
Ptroglodytes  all identical  ENSPTRG00000029751  333ISNVRLARVMLTQFAE
Mmulatta  all identical  ENSMMUG00000010677  457ISNVRLARVMLTQFAEGRLEDQL
Fcatus  all identical  ENSFCAG00000015694  457ISNVRLARVMLTQFAVGRLEEQL
Mmusculus  all identical  ENSMUSG00000025209  458ISNVRLARVMLTQFAVTRLEEQL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0032154  424TRLAATLLRQYVGYPLDDRL
Celegans  not conserved  F46G11.1  373MPEKKILHWMLVQYAGYDDLVFFLFPSHLRS
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
384635DOMAINSF4 helicase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2055 / 2055
position (AA) of stopcodon in wt / mu AA sequence 685 / 685
position of stopcodon in wt / mu cDNA 2240 / 2240
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 186 / 186
chromosome 10
strand 1
last intron/exon boundary 1920
theoretical NMD boundary in CDS 1684
length of CDS 2055
coding sequence (CDS) position 1370
cDNA position
(for ins/del: last normal base / first normal base)		 1555
gDNA position
(for ins/del: last normal base / first normal base)		 2404
chromosomal position
(for ins/del: last normal base / first normal base)		 102749527
original gDNA sequence snippet ACTAGCCCGGGTCATGCTGACACAGTTTGCCGAGGGGCGGC
altered gDNA sequence snippet ACTAGCCCGGGTCATGCTGATACAGTTTGCCGAGGGGCGGC
original cDNA sequence snippet ACTAGCCCGGGTCATGCTGACACAGTTTGCCGAGGGGCGGC
altered cDNA sequence snippet ACTAGCCCGGGTCATGCTGATACAGTTTGCCGAGGGGCGGC
wildtype AA sequence MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEAAKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLTQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKAS QEADNVLILQ DRKLVTGPGK
RYLQVSKNRF DGDVGVFPLE FNKNSLTFSI PPKNKARLKK IKDDTGPVAK KPSSGKKGAT
TQNSEICSGQ APTPDQPDTS KRSK*
mutated AA sequence MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEAAKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLIQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKAS QEADNVLILQ DRKLVTGPGK
RYLQVSKNRF DGDVGVFPLE FNKNSLTFSI PPKNKARLKK IKDDTGPVAK KPSSGKKGAT
TQNSEICSGQ APTPDQPDTS KRSK*
speed 0.97 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: 0.999998173552585 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM076376)
  • known disease mutation: rs4626 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:102749527C>TN/A show variant in all transcripts   IGV
HGNC symbol TWNK
Ensembl transcript ID ENST00000370228
Genbank transcript ID NM_001163812
UniProt peptide Q96RR1
alteration type single base exchange
alteration region CDS
DNA changes c.1370C>T
cDNA.1555C>T
g.2404C>T
AA changes T457I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 457
frameshift no
known variant Reference ID: rs80356544
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs4626 (pathogenic for Mitochondrial DNA-depletion syndrome 3, hepatocerebral|Infantile onset spinocerebellar ataxia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)

known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)
known disease mutation at this position, please check HGMD for details (HGMD ID CM076376)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9911
6.0431
(flanking)-0.6580.849
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 115
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      457ISNVRLARVMLTQFAEGRLEDQLD
mutated  not conserved    457ISNVRLARVMLIQFAEGRLEDQL
Ptroglodytes  all identical  ENSPTRG00000029751  333ISNVRLARVMLTQFAE
Mmulatta  all identical  ENSMMUG00000010677  457ISNVRLARVMLTQFAEGRLEDQL
Fcatus  all identical  ENSFCAG00000015694  457ISNVRLARVMLTQFAVGRLEEQL
Mmusculus  all identical  ENSMUSG00000025209  458ISNVRLARVMLTQFAVTRLEEQL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0032154  424TRLAATLLRQYVGYPLDDRL
Celegans  not conserved  F46G11.1  373MPEKKILHWMLVQYAGYDDLVFFLFPSHLRS
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
384635DOMAINSF4 helicase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1749 / 1749
position (AA) of stopcodon in wt / mu AA sequence 583 / 583
position of stopcodon in wt / mu cDNA 1934 / 1934
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 186 / 186
chromosome 10
strand 1
last intron/exon boundary 1964
theoretical NMD boundary in CDS 1728
length of CDS 1749
coding sequence (CDS) position 1370
cDNA position
(for ins/del: last normal base / first normal base)		 1555
gDNA position
(for ins/del: last normal base / first normal base)		 2404
chromosomal position
(for ins/del: last normal base / first normal base)		 102749527
original gDNA sequence snippet ACTAGCCCGGGTCATGCTGACACAGTTTGCCGAGGGGCGGC
altered gDNA sequence snippet ACTAGCCCGGGTCATGCTGATACAGTTTGCCGAGGGGCGGC
original cDNA sequence snippet ACTAGCCCGGGTCATGCTGACACAGTTTGCCGAGGGGCGGC
altered cDNA sequence snippet ACTAGCCCGGGTCATGCTGATACAGTTTGCCGAGGGGCGGC
wildtype AA sequence MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEAAKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLTQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKVS GL*
mutated AA sequence MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEAAKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLIQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKVS GL*
speed 0.99 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