Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999686961 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM078154)
  • known disease mutation: rs6174 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526568C>TN/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.547C>T
cDNA.684C>T
g.3082C>T
AA changes R183C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs144885874
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs6174 (pathogenic for Mitochondrial complex III deficiency, nuclear type 1|GRACILE syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM078154)

known disease mutation at this position, please check HGMD for details (HGMD ID CM078154)
known disease mutation at this position, please check HGMD for details (HGMD ID CM078154)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.9850.022
1.8010.947
(flanking)4.6151
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 increased3082wt: 0.9558 / mu: 0.9568 (marginal change - not scored)wt: GGCGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGAAT
mu: GGCGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGAAT		 ccac|GCCG
Acc increased3072wt: 0.38 / mu: 0.50wt: GGCTCTGAATGGCGTCCCTTTGGCTATCCACGCCGCCGGCG
mu: GGCTCTGAATGGCGTCCCTTTGGCTATCCATGCCGCCGGCG		 cttt|GGCT
Acc increased3080wt: 0.83 / mu: 0.93wt: ATGGCGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGA
mu: ATGGCGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGA		 atcc|ACGC
Acc marginally increased3074wt: 0.3784 / mu: 0.3840 (marginal change - not scored)wt: CTCTGAATGGCGTCCCTTTGGCTATCCACGCCGCCGGCGAC
mu: CTCTGAATGGCGTCCCTTTGGCTATCCATGCCGCCGGCGAC		 ttgg|CTAT
Acc increased3084wt: 0.73 / mu: 0.84wt: CGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGAATTC
mu: CGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGAATTC		 acgc|CGCC
Acc marginally increased3081wt: 0.3889 / mu: 0.4365 (marginal change - not scored)wt: TGGCGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGAA
mu: TGGCGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGAA		 tcca|CGCC
Acc increased3089wt: 0.42 / mu: 0.47wt: CTTTGGCTATCCACGCCGCCGGCGACCACTGAATTCTGTGG
mu: CTTTGGCTATCCATGCCGCCGGCGACCACTGAATTCTGTGG		 gccg|GCGA
distance from splice site 87
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183VGSEWRPFGYPRRRRPLNSVVLQQ
mutated  not conserved    183YPCRRRPLNSVVLQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  183YPRRRRPLNSVVLQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  183YPRRRRPLDSVVLQ
Ggallus  all identical  ENSGALG00000011386  183FPRRRRPLSSVVLE
Trubripes  all identical  ENSTRUG00000006343  183FPRRRRPLSSVVLE
Drerio  all identical  ENSDARG00000012295  183FPRRRRPLSSVVLE
Dmelanogaster  all identical  FBgn0032195  184GHPRRRRPTGSVVLD
Celegans  all identical  F54C9.6  203PRKKRDIESVILD
Xtropicalis  all identical  ENSXETG00000013844  183FPRRRRPLSSVVLE
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 547
cDNA position
(for ins/del: last normal base / first normal base)		 684
gDNA position
(for ins/del: last normal base / first normal base)		 3082
chromosomal position
(for ins/del: last normal base / first normal base)		 219526568
original gDNA sequence snippet GGCGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGAAT
altered gDNA sequence snippet GGCGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGAAT
original cDNA sequence snippet GGCGTCCCTTTGGCTATCCACGCCGCCGGCGACCACTGAAT
altered cDNA sequence snippet GGCGTCCCTTTGGCTATCCATGCCGCCGGCGACCACTGAAT
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 LEEARELALQ QEEGKTVMYT AVGSEWRPFG
YPCRRRPLNS VVLQQGLADR IVRDVQEFID NPKWYTDRGI PYRRGYLLYG PPGCGKSSFI
TALAGELEHS ICLLSLTDSS LSDDRLNHLL SVAPQQSLVL LEDVDAAFLS RDLAVENPVK
YQGLGRLTFS GLLNALDGVA STEARIVFMT TNHVDRLDPA LIRPGRVDLK EYVGYCSHWQ
LTQMFQRFYP GQAPSLAENF AEHVLRATNQ ISPAQVQGYF MLYKNDPVGA IHNAESLRR*
speed 1.13 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