Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 4.19211258387956e-11 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM116546)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:34637690T>GN/A show variant in all transcripts   IGV
HGNC symbol SIGMAR1
Ensembl transcript ID ENST00000378892
Genbank transcript ID N/A
UniProt peptide Q99720
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.40A>C
g.117A>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1800866
databasehomozygous (G/G)heterozygousallele carriers
1000G127834961
ExAC18416171801

known disease mutation at this position, please check HGMD for details (HGMD ID CM116546)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2460.999
00.992
(flanking)0.390.994
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -130) | splice site change before start ATG (at aa -124) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased110wt: 0.21 / mu: 0.34wt: GCCGTGCCAGGCCGCCCGCCGGGATGCAGTGGGCCGTGGGC
mu: GCCGTGCCAGGCCGCCCGCCGGGATGCCGTGGGCCGTGGGC		 gccg|GGAT
Acc increased128wt: 0.27 / mu: 0.46wt: CCGGGATGCAGTGGGCCGTGGGCCGGCGGTGGGCGTGGGCC
mu: CCGGGATGCCGTGGGCCGTGGGCCGGCGGTGGGCGTGGGCC		 gtgg|GCCG
distance from splice site 40
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
19TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
28REGIONTargeting to lipid droplets (By similarity).might get lost (downstream of altered splice site)
1030TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
3180TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
81101TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
102223TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
118148REGIONMediates ligand-binding.might get lost (downstream of altered splice site)
123123MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
126126MUTAGEND->G: Reduces ligand-binding. No effect on subcellular localization.might get lost (downstream of altered splice site)
138138MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
144144MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
150150MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
151151CONFLICTT -> A (in Ref. 4; AAF64280).might get lost (downstream of altered splice site)
158158MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
163163MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
168168CONFLICTT -> A (in Ref. 6; ABG29111).might get lost (downstream of altered splice site)
172172MUTAGENE->G: Reduces ligand-binding. No effect on subcellular localization.might get lost (downstream of altered splice site)
188188MUTAGEND->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
195195MUTAGEND->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
208208CONFLICTR -> W (in Ref. 5; AAV33304).might get lost (downstream of altered splice site)
213213MUTAGENE->G: No effect on ligand-binding.might get lost (downstream of altered splice site)
218218CONFLICTL -> I (in Ref. 6; ABG29111).might get lost (downstream of altered splice site)
219219CONFLICTF -> S (in Ref. 9; BAD96619).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 429 / 429
chromosome 9
strand -1
last intron/exon boundary 607
theoretical NMD boundary in CDS 128
length of CDS 405
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 40
gDNA position
(for ins/del: last normal base / first normal base)		 117
chromosomal position
(for ins/del: last normal base / first normal base)		 34637690
original gDNA sequence snippet CAGGCCGCCCGCCGGGATGCAGTGGGCCGTGGGCCGGCGGT
altered gDNA sequence snippet CAGGCCGCCCGCCGGGATGCCGTGGGCCGTGGGCCGGCGGT
original cDNA sequence snippet CAGGCCGCCCGCCGGGATGCAGTGGGCCGTGGGCCGGCGGT
altered cDNA sequence snippet CAGGCCGCCCGCCGGGATGCCGTGGGCCGTGGGCCGGCGGT
wildtype AA sequence MGAMCLLHAS LSEYVLLFGT ALGSRGHSGR YWAEISDTII SGTFHQWREG TTKSEVFYPG
ETVVHGPGEA TAVEWGPNTW MVEYGRGVIP STLAFALADT VFSTQDFLTL FYTLRSYARG
LRLELTTYLF GQDP*
mutated AA sequence N/A
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