Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.990682331384219 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000277010
Genbank transcript ID NM_005866
UniProt peptide Q99720
alteration type single base exchange
alteration region CDS
DNA changes c.5A>C
cDNA.79A>C
g.117A>C
AA changes Q2P Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 2
frameshift no
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
effectgDNA positionscorewt detection 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 79
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      2 MQWAVGRRWAWAAL
mutated  not conserved    2 MPWAVGRRWAWAALLLAVAAVL
Ptroglodytes  all identical  ENSPTRG00000020885  2 MQWAVGRRWAWAALLLAVAAVL
Mmulatta  all identical  ENSMMUG00000020774  2 MQWAVGRRWAWAALLLAVAAVL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000036078  2 MPWAAGRRWAWITLILTIIAVL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000011418  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000013205  n/a
protein features
start (aa)end (aa)featuredetails 
19TOPO_DOMCytoplasmic (Potential).lost
28REGIONTargeting to lipid droplets (By similarity).lost
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 672 / 672
position (AA) of stopcodon in wt / mu AA sequence 224 / 224
position of stopcodon in wt / mu cDNA 746 / 746
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 75 / 75
chromosome 9
strand -1
last intron/exon boundary 520
theoretical NMD boundary in CDS 395
length of CDS 672
coding sequence (CDS) position 5
cDNA position
(for ins/del: last normal base / first normal base)		 79
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 MQWAVGRRWA WAALLLAVAA VLTQVVWLWL GTQSFVFQRE EIAQLARQYA GLDHELAFSR
LIVELRRLHP GHVLPDEELQ WVFVNAGGWM GAMCLLHASL SEYVLLFGTA LGSRGHSGRY
WAEISDTIIS GTFHQWREGT TKSEVFYPGE TVVHGPGEAT AVEWGPNTWM VEYGRGVIPS
TLAFALADTV FSTQDFLTLF YTLRSYARGL RLELTTYLFG QDP*
mutated AA sequence MPWAVGRRWA WAALLLAVAA VLTQVVWLWL GTQSFVFQRE EIAQLARQYA GLDHELAFSR
LIVELRRLHP GHVLPDEELQ WVFVNAGGWM GAMCLLHASL SEYVLLFGTA LGSRGHSGRY
WAEISDTIIS GTFHQWREGT TKSEVFYPGE TVVHGPGEAT AVEWGPNTWM VEYGRGVIPS
TLAFALADTV FSTQDFLTLF YTLRSYARGL RLELTTYLFG QDP*
speed 1.09 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