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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000366684
Querying Taster for transcript #2: ENST00000308794
Querying Taster for transcript #3: ENST00000366682
Querying Taster for transcript #4: ENST00000366683
MT speed 0 s - this script 4.346359 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACTA1disease_causing_automatic0.999999999990101simple_aaeaffected0L96Psingle base exchangers121909519show file
ACTA1disease_causing_automatic0.999999999990101simple_aaeaffected0L96Psingle base exchangers121909519show file
ACTA1disease_causing_automatic0.999999999990101simple_aaeaffected0L96Psingle base exchangers121909519show file
ACTA1disease_causing_automatic1without_aaeaffected0single base exchangers121909519show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999990101 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992118)
  • known disease mutation: rs18279 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568470A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTA1
Ensembl transcript ID ENST00000308794
Genbank transcript ID N/A
UniProt peptide P68133
alteration type single base exchange
alteration region CDS
DNA changes c.287T>C
cDNA.390T>C
g.1376T>C
AA changes L96P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 96
frameshift no
known variant Reference ID: rs121909519
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18279 (pathogenic for Nemaline myopathy 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8210.771
4.6591
(flanking)5.641
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1373wt: 0.46 / mu: 0.62wt: GCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGG
mu: GCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGG		 acga|GCTT
Acc increased1370wt: 0.24 / mu: 0.34wt: CTGGCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCG
mu: CTGGCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCG		 acaa|CGAG
Donor marginally increased1373wt: 0.8504 / mu: 0.9218 (marginal change - not scored)wt: CAACGAGCTTCGCGT
mu: CAACGAGCCTCGCGT		 ACGA|gctt
Donor increased1368wt: 0.38 / mu: 0.47wt: TTCTACAACGAGCTT
mu: TTCTACAACGAGCCT		 CTAC|aacg
distance from splice site 65
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      96EKIWHHTFYNELRVAPEEHPTLLT
mutated  not conserved    96EKIWHHTFYNEPRVAPEEHPTLL
Ptroglodytes  all identical  ENSPTRG00000002086  96EKIWHHTFYNELRVAPEEHPTLL
Mmulatta  all identical  ENSMMUG00000022086  96EKIWHHTFYNELRVAPEEHPTLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  96EKIWHHTFYNELRVAPEEHPTLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  96EKIWHHSFYNELRVAPEEHPTLL
Drerio  all identical  ENSDARG00000037840  96EKIWHHTFYNELRVAPEEHPTLL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
100102HELIXmight get lost (downstream of altered splice site)
105109STRANDmight get lost (downstream of altered splice site)
115127HELIXmight get lost (downstream of altered splice site)
132138STRANDmight get lost (downstream of altered splice site)
139146HELIXmight get lost (downstream of altered splice site)
154157STRANDmight get lost (downstream of altered splice site)
162165STRANDmight get lost (downstream of altered splice site)
174176HELIXmight get lost (downstream of altered splice site)
178180STRANDmight get lost (downstream of altered splice site)
186197HELIXmight get lost (downstream of altered splice site)
193193MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
205218HELIXmight get lost (downstream of altered splice site)
225234HELIXmight get lost (downstream of altered splice site)
240243STRANDmight get lost (downstream of altered splice site)
242242MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
249252STRANDmight get lost (downstream of altered splice site)
255264HELIXmight get lost (downstream of altered splice site)
266268HELIXmight get lost (downstream of altered splice site)
277284HELIXmight get lost (downstream of altered splice site)
289291TURNmight get lost (downstream of altered splice site)
292297HELIXmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
328328MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
330330MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
335338TURNmight get lost (downstream of altered splice site)
340342TURNmight get lost (downstream of altered splice site)
347350HELIXmight get lost (downstream of altered splice site)
354357HELIXmight get lost (downstream of altered splice site)
358360STRANDmight get lost (downstream of altered splice site)
361366HELIXmight get lost (downstream of altered splice site)
371375HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 864 / 864
position (AA) of stopcodon in wt / mu AA sequence 288 / 288
position of stopcodon in wt / mu cDNA 967 / 967
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 104 / 104
chromosome 1
strand -1
last intron/exon boundary 824
theoretical NMD boundary in CDS 670
length of CDS 864
coding sequence (CDS) position 287
cDNA position
(for ins/del: last normal base / first normal base)		 390
gDNA position
(for ins/del: last normal base / first normal base)		 1376
chromosomal position
(for ins/del: last normal base / first normal base)		 229568470
original gDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered gDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
original cDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered cDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
wildtype AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREI
VRDIKEKLCY VALDFENEMA TAASSSSLEK SYELPDGQVI TIGNERFRCP ETLFQPSFIG
MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEIT ALAPSTMKIK
IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF*
mutated AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNEPRVAP EEHPTLLTEA PLNPKANREI
VRDIKEKLCY VALDFENEMA TAASSSSLEK SYELPDGQVI TIGNERFRCP ETLFQPSFIG
MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEIT ALAPSTMKIK
IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF*
speed 0.84 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: 0.999999999990101 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992118)
  • known disease mutation: rs18279 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568470A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTA1
Ensembl transcript ID ENST00000366684
Genbank transcript ID NM_001100
UniProt peptide P68133
alteration type single base exchange
alteration region CDS
DNA changes c.287T>C
cDNA.390T>C
g.1376T>C
AA changes L96P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 96
frameshift no
known variant Reference ID: rs121909519
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18279 (pathogenic for Nemaline myopathy 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8210.771
4.6591
(flanking)5.641
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1373wt: 0.46 / mu: 0.62wt: GCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGG
mu: GCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGG		 acga|GCTT
Acc increased1370wt: 0.24 / mu: 0.34wt: CTGGCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCG
mu: CTGGCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCG		 acaa|CGAG
Donor marginally increased1373wt: 0.8504 / mu: 0.9218 (marginal change - not scored)wt: CAACGAGCTTCGCGT
mu: CAACGAGCCTCGCGT		 ACGA|gctt
Donor increased1368wt: 0.38 / mu: 0.47wt: TTCTACAACGAGCTT
mu: TTCTACAACGAGCCT		 CTAC|aacg
distance from splice site 158
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      96EKIWHHTFYNELRVAPEEHPTLLT
mutated  not conserved    96EKIWHHTFYNEPRVAPEEHPTLL
Ptroglodytes  all identical  ENSPTRG00000002086  96EKIWHHTFYNELRVAPEEHPTLL
Mmulatta  all identical  ENSMMUG00000022086  96EKIWHHTFYNELRVAPEEHPTLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  96EKIWHHTFYNELRVAPEEHPTLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  96EKIWHHSFYNELRVAPEEHPTLL
Drerio  all identical  ENSDARG00000037840  96EKIWHHTFYNELRVAPEEHPTLL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
100102HELIXmight get lost (downstream of altered splice site)
105109STRANDmight get lost (downstream of altered splice site)
115127HELIXmight get lost (downstream of altered splice site)
132138STRANDmight get lost (downstream of altered splice site)
139146HELIXmight get lost (downstream of altered splice site)
154157STRANDmight get lost (downstream of altered splice site)
162165STRANDmight get lost (downstream of altered splice site)
174176HELIXmight get lost (downstream of altered splice site)
178180STRANDmight get lost (downstream of altered splice site)
186197HELIXmight get lost (downstream of altered splice site)
193193MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
205218HELIXmight get lost (downstream of altered splice site)
225234HELIXmight get lost (downstream of altered splice site)
240243STRANDmight get lost (downstream of altered splice site)
242242MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
249252STRANDmight get lost (downstream of altered splice site)
255264HELIXmight get lost (downstream of altered splice site)
266268HELIXmight get lost (downstream of altered splice site)
277284HELIXmight get lost (downstream of altered splice site)
289291TURNmight get lost (downstream of altered splice site)
292297HELIXmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
328328MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
330330MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
335338TURNmight get lost (downstream of altered splice site)
340342TURNmight get lost (downstream of altered splice site)
347350HELIXmight get lost (downstream of altered splice site)
354357HELIXmight get lost (downstream of altered splice site)
358360STRANDmight get lost (downstream of altered splice site)
361366HELIXmight get lost (downstream of altered splice site)
371375HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1134 / 1134
position (AA) of stopcodon in wt / mu AA sequence 378 / 378
position of stopcodon in wt / mu cDNA 1237 / 1237
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 104 / 104
chromosome 1
strand -1
last intron/exon boundary 1094
theoretical NMD boundary in CDS 940
length of CDS 1134
coding sequence (CDS) position 287
cDNA position
(for ins/del: last normal base / first normal base)		 390
gDNA position
(for ins/del: last normal base / first normal base)		 1376
chromosomal position
(for ins/del: last normal base / first normal base)		 229568470
original gDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered gDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
original cDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered cDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
wildtype AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT
KQEYDEAGPS IVHRKCF*
mutated AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNEPRVAP EEHPTLLTEA PLNPKANREK
MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL
DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK
SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV
MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT
KQEYDEAGPS IVHRKCF*
speed 0.77 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: 0.999999999990101 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992118)
  • known disease mutation: rs18279 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568470A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTA1
Ensembl transcript ID ENST00000366683
Genbank transcript ID N/A
UniProt peptide P68133
alteration type single base exchange
alteration region CDS
DNA changes c.287T>C
cDNA.394T>C
g.1376T>C
AA changes L96P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 96
frameshift no
known variant Reference ID: rs121909519
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18279 (pathogenic for Nemaline myopathy 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8210.771
4.6591
(flanking)5.641
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1373wt: 0.46 / mu: 0.62wt: GCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGG
mu: GCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGG		 acga|GCTT
Acc increased1370wt: 0.24 / mu: 0.34wt: CTGGCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCG
mu: CTGGCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCG		 acaa|CGAG
Donor marginally increased1373wt: 0.8504 / mu: 0.9218 (marginal change - not scored)wt: CAACGAGCTTCGCGT
mu: CAACGAGCCTCGCGT		 ACGA|gctt
Donor increased1368wt: 0.38 / mu: 0.47wt: TTCTACAACGAGCTT
mu: TTCTACAACGAGCCT		 CTAC|aacg
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      96EKIWHHTFYNELRVAPEEHPTLLT
mutated  not conserved    96EKIWHHTFYNEPRVAPEEHPTLL
Ptroglodytes  all identical  ENSPTRG00000002086  96EKIWHHTFYNELRVAPEEHPTLL
Mmulatta  all identical  ENSMMUG00000022086  96EKIWHHTFYNELRVAPEEHPTLL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  96EKIWHHTFYNELRVAPEEHPTLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  96EKIWHHSFYNELRVAPEEHPTLL
Drerio  all identical  ENSDARG00000037840  96EKIWHHTFYNELRVAPEEHPTLL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
100102HELIXmight get lost (downstream of altered splice site)
105109STRANDmight get lost (downstream of altered splice site)
115127HELIXmight get lost (downstream of altered splice site)
132138STRANDmight get lost (downstream of altered splice site)
139146HELIXmight get lost (downstream of altered splice site)
154157STRANDmight get lost (downstream of altered splice site)
162165STRANDmight get lost (downstream of altered splice site)
174176HELIXmight get lost (downstream of altered splice site)
178180STRANDmight get lost (downstream of altered splice site)
186197HELIXmight get lost (downstream of altered splice site)
193193MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
205218HELIXmight get lost (downstream of altered splice site)
225234HELIXmight get lost (downstream of altered splice site)
240243STRANDmight get lost (downstream of altered splice site)
242242MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
249252STRANDmight get lost (downstream of altered splice site)
255264HELIXmight get lost (downstream of altered splice site)
266268HELIXmight get lost (downstream of altered splice site)
277284HELIXmight get lost (downstream of altered splice site)
289291TURNmight get lost (downstream of altered splice site)
292297HELIXmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
328328MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
330330MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
335338TURNmight get lost (downstream of altered splice site)
340342TURNmight get lost (downstream of altered splice site)
347350HELIXmight get lost (downstream of altered splice site)
354357HELIXmight get lost (downstream of altered splice site)
358360STRANDmight get lost (downstream of altered splice site)
361366HELIXmight get lost (downstream of altered splice site)
371375HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 870 / 870
position (AA) of stopcodon in wt / mu AA sequence 290 / 290
position of stopcodon in wt / mu cDNA 977 / 977
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 108 / 108
chromosome 1
strand -1
last intron/exon boundary 834
theoretical NMD boundary in CDS 676
length of CDS 870
coding sequence (CDS) position 287
cDNA position
(for ins/del: last normal base / first normal base)		 394
gDNA position
(for ins/del: last normal base / first normal base)		 1376
chromosomal position
(for ins/del: last normal base / first normal base)		 229568470
original gDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered gDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
original cDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered cDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
wildtype AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANPER
EIVRDIKEKL CYVALDFENE MATAASSSSL EKSYELPDGQ VITIGNERFR CPETLFQPSF
IGMESAGIHE TTYNSIMKCD IDIRKDLYAN NVMSGGTTMY PGIADRMQKE ITALAPSTMK
IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF*
mutated AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNEPRVAP EEHPTLLTEA PLNPKANPER
EIVRDIKEKL CYVALDFENE MATAASSSSL EKSYELPDGQ VITIGNERFR CPETLFQPSF
IGMESAGIHE TTYNSIMKCD IDIRKDLYAN NVMSGGTTMY PGIADRMQKE ITALAPSTMK
IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF*
speed 0.81 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 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM992118)
  • known disease mutation: rs18279 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568470A>GN/A show variant in all transcripts   IGV
HGNC symbol ACTA1
Ensembl transcript ID ENST00000366682
Genbank transcript ID N/A
UniProt peptide P68133
alteration type single base exchange
alteration region intron
DNA changes g.1376T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121909519
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18279 (pathogenic for Nemaline myopathy 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992118)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8210.771
4.6591
(flanking)5.641
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1373wt: 0.46 / mu: 0.62wt: GCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGG
mu: GCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGG		 acga|GCTT
Acc increased1370wt: 0.24 / mu: 0.34wt: CTGGCACCACACCTTCTACAACGAGCTTCGCGTGGCTCCCG
mu: CTGGCACCACACCTTCTACAACGAGCCTCGCGTGGCTCCCG		 acaa|CGAG
Donor marginally increased1373wt: 0.8504 / mu: 0.9218 (marginal change - not scored)wt: CAACGAGCTTCGCGT
mu: CAACGAGCCTCGCGT		 ACGA|gctt
Donor increased1368wt: 0.38 / mu: 0.47wt: TTCTACAACGAGCTT
mu: TTCTACAACGAGCCT		 CTAC|aacg
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
8193HELIXmight get lost (downstream of altered splice site)
9393MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
100102HELIXmight get lost (downstream of altered splice site)
105109STRANDmight get lost (downstream of altered splice site)
115127HELIXmight get lost (downstream of altered splice site)
132138STRANDmight get lost (downstream of altered splice site)
139146HELIXmight get lost (downstream of altered splice site)
154157STRANDmight get lost (downstream of altered splice site)
162165STRANDmight get lost (downstream of altered splice site)
174176HELIXmight get lost (downstream of altered splice site)
178180STRANDmight get lost (downstream of altered splice site)
186197HELIXmight get lost (downstream of altered splice site)
193193MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
205218HELIXmight get lost (downstream of altered splice site)
225234HELIXmight get lost (downstream of altered splice site)
240243STRANDmight get lost (downstream of altered splice site)
242242MOD_RESPhosphotyrosine (By similarity).might get lost (downstream of altered splice site)
249252STRANDmight get lost (downstream of altered splice site)
255264HELIXmight get lost (downstream of altered splice site)
266268HELIXmight get lost (downstream of altered splice site)
277284HELIXmight get lost (downstream of altered splice site)
289291TURNmight get lost (downstream of altered splice site)
292297HELIXmight get lost (downstream of altered splice site)
299302STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
328328MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
330330MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
335338TURNmight get lost (downstream of altered splice site)
340342TURNmight get lost (downstream of altered splice site)
347350HELIXmight get lost (downstream of altered splice site)
354357HELIXmight get lost (downstream of altered splice site)
358360STRANDmight get lost (downstream of altered splice site)
361366HELIXmight get lost (downstream of altered splice site)
371375HELIXmight 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 104 / 104
chromosome 1
strand -1
last intron/exon boundary 989
theoretical NMD boundary in CDS 835
length of CDS 1029
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)		 1376
chromosomal position
(for ins/del: last normal base / first normal base)		 229568470
original gDNA sequence snippet CCACACCTTCTACAACGAGCTTCGCGTGGCTCCCGAGGAGC
altered gDNA sequence snippet CCACACCTTCTACAACGAGCCTCGCGTGGCTCCCGAGGAGC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA
QSKRGILTLK YPIEHGIITK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL
DSGDGVTHNV PIYEGYALPH AIMRLDLAGR DLTDYLMKIL TERGYSFVTT AEREIVRDIK
EKLCYVALDF ENEMATAASS SSLEKSYELP DGQVITIGNE RFRCPETLFQ PSFIGMESAG
IHETTYNSIM KCDIDIRKDL YANNVMSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP
ERKYSVWIGG SILASLSTFQ QMWITKQEYD EAGPSIVHRK CF*
mutated AA sequence N/A
speed 0.63 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
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