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 3.42 s - this script 4.797824 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ACTA1disease_causing_automatic0.999997016677978simple_aaeaffected0G17Rsingle base exchangers121909521show file
ACTA1disease_causing_automatic0.999997016677978simple_aaeaffected0G17Rsingle base exchangers121909521show file
ACTA1disease_causing_automatic0.999997016677978simple_aaeaffected0G17Rsingle base exchangers121909521show file
ACTA1disease_causing_automatic0.999997016677978simple_aaeaffected0G17Rsingle base exchangers121909521show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997016677978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992116)
  • known disease mutation: rs18281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568814C>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.49G>C
cDNA.152G>C
g.1032G>C
AA changes G17R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
known variant Reference ID: rs121909521
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18281 (pathogenic for Congenital myopathy with excess of thin filaments) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4951
3.8811
(flanking)-0.2960.978
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 increased1027wt: 0.3162 / mu: 0.3272 (marginal change - not scored)wt: CGCCCTCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCG
mu: CGCCCTCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCG		 atgg|CTCC
Donor marginally increased1037wt: 0.8533 / mu: 0.9489 (marginal change - not scored)wt: GGCCTGGTGAAAGCC
mu: CGCCTGGTGAAAGCC		 CCTG|gtga
Acc gained10360.59mu: GTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTCGCCG gcct|GGTG
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17ETTALVCDNGSGLVKAGFAGDDAP
mutated  not conserved    17ETTALVCDNGSRLVKAGFAGDDA
Ptroglodytes  all identical  ENSPTRG00000002086  17ETTALVCDNGSGLVKAGFAGDDA
Mmulatta  all identical  ENSMMUG00000022086  17ETTALVCDNGSGLVKAGFAGDDA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  17ETTALVCDNGSGLVKAGFAGDDA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  17ETTALVCDNGSGLVKAGFAGDDA
Drerio  all identical  ENSDARG00000037840  17ETTALVCDNGSGLVKAGFAGDDA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1921STRANDmight get lost (downstream of altered splice site)
3033STRANDmight get lost (downstream of altered splice site)
4646MOD_RESMethionine sulfoxide (By similarity).might get lost (downstream of altered splice site)
5555MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
5961TURNmight get lost (downstream of altered splice site)
6363MOD_RESN6-malonyllysine; alternate.might get lost (downstream of altered splice site)
6363MOD_RESN6-acetyllysine; alternate.might get lost (downstream of altered splice site)
7070MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
7575MOD_RESTele-methylhistidine (By similarity).might get lost (downstream of altered splice site)
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 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 49
cDNA position
(for ins/del: last normal base / first normal base)		 152
gDNA position
(for ins/del: last normal base / first normal base)		 1032
chromosomal position
(for ins/del: last normal base / first normal base)		 229568814
original gDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered gDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
original cDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered cDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
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 VCDNGSRLVK 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*
speed 1.07 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: 0.999997016677978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992116)
  • known disease mutation: rs18281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568814C>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.49G>C
cDNA.152G>C
g.1032G>C
AA changes G17R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
known variant Reference ID: rs121909521
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18281 (pathogenic for Congenital myopathy with excess of thin filaments) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4951
3.8811
(flanking)-0.2960.978
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 increased1027wt: 0.3162 / mu: 0.3272 (marginal change - not scored)wt: CGCCCTCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCG
mu: CGCCCTCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCG		 atgg|CTCC
Donor marginally increased1037wt: 0.8533 / mu: 0.9489 (marginal change - not scored)wt: GGCCTGGTGAAAGCC
mu: CGCCTGGTGAAAGCC		 CCTG|gtga
Acc gained10360.59mu: GTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTCGCCG gcct|GGTG
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17ETTALVCDNGSGLVKAGFAGDDAP
mutated  not conserved    17ETTALVCDNGSRLVKAGFAGDDA
Ptroglodytes  all identical  ENSPTRG00000002086  17ETTALVCDNGSGLVKAGFAGDDA
Mmulatta  all identical  ENSMMUG00000022086  17ETTALVCDNGSGLVKAGFAGDDA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  17ETTALVCDNGSGLVKAGFAGDDA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  17ETTALVCDNGSGLVKAGFAGDDA
Drerio  all identical  ENSDARG00000037840  17ETTALVCDNGSGLVKAGFAGDDA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1921STRANDmight get lost (downstream of altered splice site)
3033STRANDmight get lost (downstream of altered splice site)
4646MOD_RESMethionine sulfoxide (By similarity).might get lost (downstream of altered splice site)
5555MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
5961TURNmight get lost (downstream of altered splice site)
6363MOD_RESN6-malonyllysine; alternate.might get lost (downstream of altered splice site)
6363MOD_RESN6-acetyllysine; alternate.might get lost (downstream of altered splice site)
7070MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
7575MOD_RESTele-methylhistidine (By similarity).might get lost (downstream of altered splice site)
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 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 49
cDNA position
(for ins/del: last normal base / first normal base)		 152
gDNA position
(for ins/del: last normal base / first normal base)		 1032
chromosomal position
(for ins/del: last normal base / first normal base)		 229568814
original gDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered gDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
original cDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered cDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
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 VCDNGSRLVK 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*
speed 0.80 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: 0.999997016677978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992116)
  • known disease mutation: rs18281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568814C>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.49G>C
cDNA.156G>C
g.1032G>C
AA changes G17R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
known variant Reference ID: rs121909521
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18281 (pathogenic for Congenital myopathy with excess of thin filaments) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4951
3.8811
(flanking)-0.2960.978
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 increased1027wt: 0.3162 / mu: 0.3272 (marginal change - not scored)wt: CGCCCTCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCG
mu: CGCCCTCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCG		 atgg|CTCC
Donor marginally increased1037wt: 0.8533 / mu: 0.9489 (marginal change - not scored)wt: GGCCTGGTGAAAGCC
mu: CGCCTGGTGAAAGCC		 CCTG|gtga
Acc gained10360.59mu: GTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTCGCCG gcct|GGTG
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17ETTALVCDNGSGLVKAGFAGDDAP
mutated  not conserved    17ETTALVCDNGSRLVKAGFAGDDA
Ptroglodytes  all identical  ENSPTRG00000002086  17ETTALVCDNGSGLVKAGFAGDDA
Mmulatta  all identical  ENSMMUG00000022086  17ETTALVCDNGSGLVKAGFAGDDA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  17ETTALVCDNGSGLVKAGFAGDDA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  17ETTALVCDNGSGLVKAGFAGDDA
Drerio  all identical  ENSDARG00000037840  17ETTALVCDNGSGLVKAGFAGDDA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1921STRANDmight get lost (downstream of altered splice site)
3033STRANDmight get lost (downstream of altered splice site)
4646MOD_RESMethionine sulfoxide (By similarity).might get lost (downstream of altered splice site)
5555MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
5961TURNmight get lost (downstream of altered splice site)
6363MOD_RESN6-malonyllysine; alternate.might get lost (downstream of altered splice site)
6363MOD_RESN6-acetyllysine; alternate.might get lost (downstream of altered splice site)
7070MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
7575MOD_RESTele-methylhistidine (By similarity).might get lost (downstream of altered splice site)
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 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 49
cDNA position
(for ins/del: last normal base / first normal base)		 156
gDNA position
(for ins/del: last normal base / first normal base)		 1032
chromosomal position
(for ins/del: last normal base / first normal base)		 229568814
original gDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered gDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
original cDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered cDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
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 VCDNGSRLVK 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*
speed 0.78 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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999997016677978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992116)
  • known disease mutation: rs18281 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:229568814C>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 CDS
DNA changes c.49G>C
cDNA.152G>C
g.1032G>C
AA changes G17R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
known variant Reference ID: rs121909521
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18281 (pathogenic for Congenital myopathy with excess of thin filaments) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.4951
3.8811
(flanking)-0.2960.978
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 increased1027wt: 0.3162 / mu: 0.3272 (marginal change - not scored)wt: CGCCCTCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCG
mu: CGCCCTCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCG		 atgg|CTCC
Donor marginally increased1037wt: 0.8533 / mu: 0.9489 (marginal change - not scored)wt: GGCCTGGTGAAAGCC
mu: CGCCTGGTGAAAGCC		 CCTG|gtga
Acc gained10360.59mu: GTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTCGCCG gcct|GGTG
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17ETTALVCDNGSGLVKAGFAGDDAP
mutated  not conserved    17ETTALVCDNGSRLVKAGFAGDDA
Ptroglodytes  all identical  ENSPTRG00000002086  17ETTALVCDNGSGLVKAGFAGDDA
Mmulatta  all identical  ENSMMUG00000022086  17ETTALVCDNGSGLVKAGFAGDDA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000031972  17ETTALVCDNGSGLVKAGFAGDDA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000014318  17ETTALVCDNGSGLVKAGFAGDDA
Drerio  all identical  ENSDARG00000037840  17ETTALVCDNGSGLVKAGFAGDDA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1921STRANDmight get lost (downstream of altered splice site)
3033STRANDmight get lost (downstream of altered splice site)
4646MOD_RESMethionine sulfoxide (By similarity).might get lost (downstream of altered splice site)
5555MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
5961TURNmight get lost (downstream of altered splice site)
6363MOD_RESN6-malonyllysine; alternate.might get lost (downstream of altered splice site)
6363MOD_RESN6-acetyllysine; alternate.might get lost (downstream of altered splice site)
7070MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
7575MOD_RESTele-methylhistidine (By similarity).might get lost (downstream of altered splice site)
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1029 / 1029
position (AA) of stopcodon in wt / mu AA sequence 343 / 343
position of stopcodon in wt / mu cDNA 1132 / 1132
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 49
cDNA position
(for ins/del: last normal base / first normal base)		 152
gDNA position
(for ins/del: last normal base / first normal base)		 1032
chromosomal position
(for ins/del: last normal base / first normal base)		 229568814
original gDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered gDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
original cDNA sequence snippet TCGTGTGCGACAATGGCTCCGGCCTGGTGAAAGCCGGCTTC
altered cDNA sequence snippet TCGTGTGCGACAATGGCTCCCGCCTGGTGAAAGCCGGCTTC
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 MCDEDETTAL VCDNGSRLVK 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*
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

Problems