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 7 transcript(s)...
Querying Taster for transcript #1: ENST00000359273
Querying Taster for transcript #2: ENST00000392109
Querying Taster for transcript #3: ENST00000392110
Querying Taster for transcript #4: ENST00000392111
Querying Taster for transcript #5: ENST00000412366
Querying Taster for transcript #6: ENST00000439945
Querying Taster for transcript #7: ENST00000431802
MT speed 0 s - this script 5.27792 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file
BCS1Ldisease_causing_automatic0.999999944059374simple_aaeaffected0R155Psingle base exchangers121908573show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000359273
Genbank transcript ID NM_001079866
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.601G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1397 / 1397
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 138 / 138
chromosome 2
strand 1
last intron/exon boundary 1145
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 601
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.89 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000392109
Genbank transcript ID NM_001257343
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.730G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1526 / 1526
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 267 / 267
chromosome 2
strand 1
last intron/exon boundary 1274
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 730
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 1.01 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000392110
Genbank transcript ID NM_001257342
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.673G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1469 / 1469
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 210 / 210
chromosome 2
strand 1
last intron/exon boundary 1217
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 673
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.82 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000392111
Genbank transcript ID NM_004328
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.731G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1527 / 1527
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 268 / 268
chromosome 2
strand 1
last intron/exon boundary 1275
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 731
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.76 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000412366
Genbank transcript ID NM_001257344
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.577G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1373 / 1373
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 114 / 114
chromosome 2
strand 1
last intron/exon boundary 1121
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 577
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.61 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000439945
Genbank transcript ID N/A
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.669G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1465 / 1465
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 206 / 206
chromosome 2
strand 1
last intron/exon boundary 1213
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 669
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.44 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: 0.999999944059374 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012736)
  • known disease mutation: rs6165 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526485G>CN/A show variant in all transcripts   IGV
HGNC symbol BCS1L
Ensembl transcript ID ENST00000431802
Genbank transcript ID N/A
UniProt peptide Q9Y276
alteration type single base exchange
alteration region CDS
DNA changes c.464G>C
cDNA.1163G>C
g.2999G>C
AA changes R155P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 155
frameshift no
known variant Reference ID: rs121908573
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6165 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012736)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5780.967
4.3921
(flanking)0.4661
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 increased3000wt: 0.9166 / mu: 0.9274 (marginal change - not scored)wt: ATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGA
mu: ATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGA		 tcga|GAGC
Acc marginally increased3002wt: 0.5189 / mu: 0.5315 (marginal change - not scored)wt: CTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGGAGG
mu: CTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAGG		 gaga|GCTA
Acc marginally increased2993wt: 0.9751 / mu: 0.9776 (marginal change - not scored)wt: TTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGC
mu: TTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGC		 tccc|AGCT
Acc marginally increased2990wt: 0.9015 / mu: 0.9020 (marginal change - not scored)wt: GCTTTATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCT
mu: GCTTTATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCT		 cctt|CCCA
Acc marginally increased2999wt: 0.7434 / mu: 0.7815 (marginal change - not scored)wt: CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
mu: CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG		 ctcg|AGAG
Acc marginally decreased2995wt: 0.9817 / mu: 0.9745 (marginal change - not scored)wt: ATCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAG
mu: ATCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAG		 ccag|CTCG
Acc marginally increased2996wt: 0.7018 / mu: 0.7611 (marginal change - not scored)wt: TCTCATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGC
mu: TCTCATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGC		 cagc|TCGA
Donor increased3002wt: 0.57 / mu: 0.77wt: TCGAGAGCTAGCCTT
mu: TCCAGAGCTAGCCTT		 GAGA|gcta
Donor lost29950.94wt: TCCCAGCTCGAGAGC CCAG|ctcg
Acc gained30010.93mu: TCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGGAG ccag|AGCT
Donor gained29970.57mu: CCAGCTCCAGAGCTA AGCT|ccag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      155RKVFFNILEEARELALQQEEGKTV
mutated  not conserved    155RKVFFNILEEAPELALQQEEGKT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  155RKVFFNILEEARELALQQEEGKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  155RKVFFNILEEARALALQQEEGKT
Ggallus  all identical  ENSGALG00000011386  155REIFFNILQEARELALQQQEGRT
Trubripes  all identical  ENSTRUG00000006343  155RQIFFNILQEARELALKQEEGRT
Drerio  all identical  ENSDARG00000012295  155RQTFFNILQEARELALKQEEGRT
Dmelanogaster  all identical  FBgn0032195  156KGIYFDILEEARQLALEATEGKT
Celegans  not conserved  F54C9.6  174VKFFKRMLEQSAKEAIDNAETGL
Xtropicalis  all identical  ENSXETG00000013844  155RDIFFNILQEARELALKQQVGKT
protein features
start (aa)end (aa)featuredetails 
33419TOPO_DOMMitochondrial matrix (Potential).lost
181181MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
230237NP_BINDATP (Potential).might get lost (downstream of altered splice site)
394394CONFLICTA -> T (in Ref. 6; CAE11877).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1260 / 1260
position (AA) of stopcodon in wt / mu AA sequence 420 / 420
position of stopcodon in wt / mu cDNA 1959 / 1959
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 700 / 700
chromosome 2
strand 1
last intron/exon boundary 1707
theoretical NMD boundary in CDS 957
length of CDS 1260
coding sequence (CDS) position 464
cDNA position
(for ins/del: last normal base / first normal base)		 1163
gDNA position
(for ins/del: last normal base / first normal base)		 2999
chromosomal position
(for ins/del: last normal base / first normal base)		 219526485
original gDNA sequence snippet CATCTTCTCCTTCCCAGCTCGAGAGCTAGCCTTGCAGCAGG
altered gDNA sequence snippet CATCTTCTCCTTCCCAGCTCCAGAGCTAGCCTTGCAGCAGG
original cDNA sequence snippet CAACATCCTGGAGGAAGCTCGAGAGCTAGCCTTGCAGCAGG
altered cDNA sequence snippet CAACATCCTGGAGGAAGCTCCAGAGCTAGCCTTGCAGCAGG
wildtype AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
mutated AA sequence MPLSDFILAL KDNPYFGAGF GLVGVGTALA LARKGVQLGL VAFRRHYMIT LEVPARDRSY
AWLLSWLTRH STRTQHLSVE TSYLQHESGR ISTKFEFVPS PGNHFIWYRG KWIRVERSRE
MQMIDLQTGT PWESVTFTAL GTDRKVFFNI LEEAPELALQ QEEGKTVMYT AVGSEWRPFG
YPRRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 0.86 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