Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999996 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012735)
  • known disease mutation: rs6164 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:219526006C>TN/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.296C>T
cDNA.995C>T
g.2520C>T
AA changes P99L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 99
frameshift no
known variant Reference ID: rs121908572
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs6164 (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 CM012735)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012735)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012735)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.1411
6.1411
(flanking)0.3330.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2528wt: 0.21 / mu: 0.28wt: TTGAATTTGTCCCCAGCCCTGGAAACCATTTTATCTGGTAA
mu: TTGAATTTGTCCTCAGCCCTGGAAACCATTTTATCTGGTAA		 cctg|GAAA
Acc increased2522wt: 0.71 / mu: 0.79wt: CTAAGTTTGAATTTGTCCCCAGCCCTGGAAACCATTTTATC
mu: CTAAGTTTGAATTTGTCCTCAGCCCTGGAAACCATTTTATC		 ccca|GCCC
Acc increased2529wt: 0.20 / mu: 0.31wt: TGAATTTGTCCCCAGCCCTGGAAACCATTTTATCTGGTAAG
mu: TGAATTTGTCCTCAGCCCTGGAAACCATTTTATCTGGTAAG		 ctgg|AAAC
distance from splice site 25
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      99SGRISTKFEFVPSPGNHFIWYRGK
mutated  not conserved    99SGRISTKFEFVLSPGNHFIWYRG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000006740  99SGRISTKFEFVPSPGNHFIWYRG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026172  99SGRISTKFEFIPSPGNHFIWYQG
Ggallus  all identical  ENSGALG00000011386  99SGRVSTKFDFVPSPGNHFIWYQK
Trubripes  all identical  ENSTRUG00000006343  99SGRVHTQFDFHPSPGNHIIWYGR
Drerio  all identical  ENSDARG00000012295  99SGKVHTQFDFHPSPGNHIIWYGR
Dmelanogaster  all identical  FBgn0032195  99NGTIKTSYDFIPSIGKHLFQYKG
Celegans  all identical  F54C9.6  117SGKTELSISFLPGHGTHFFVHDY
Xtropicalis  all identical  ENSXETG00000013844  99SGRISTKFDFVPSPGNHFIWYKS
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 296
cDNA position
(for ins/del: last normal base / first normal base)		 995
gDNA position
(for ins/del: last normal base / first normal base)		 2520
chromosomal position
(for ins/del: last normal base / first normal base)		 219526006
original gDNA sequence snippet CACTAAGTTTGAATTTGTCCCCAGCCCTGGAAACCATTTTA
altered gDNA sequence snippet CACTAAGTTTGAATTTGTCCTCAGCCCTGGAAACCATTTTA
original cDNA sequence snippet CACTAAGTTTGAATTTGTCCCCAGCCCTGGAAACCATTTTA
altered cDNA sequence snippet CACTAAGTTTGAATTTGTCCTCAGCCCTGGAAACCATTTTA
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 ISTKFEFVLS 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*
speed 0.96 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