Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM001382)
  • known disease mutation: rs2740 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61723364G>AN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000301774
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.680G>A
g.6072G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918284
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC022

known disease mutation: rs2740 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|Vitreoretinochoroidopathy|Bestrophinopathy, autosomal recessive|Stargardt disease|Retinitis Pigmentosa, Recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)5.8191
5.8191
(flanking)4.1861
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -24) | splice site change before start ATG (at aa -23) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased6073wt: 0.4837 / mu: 0.4926 (marginal change - not scored)wt: GGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCTA
mu: GGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCTA		 gcgc|AGCG
Donor increased6076wt: 0.26 / mu: 0.53wt: CGCAGCGTCAGCACC
mu: CACAGCGTCAGCACC		 CAGC|gtca
Donor marginally increased6069wt: 0.8590 / mu: 0.8617 (marginal change - not scored)wt: CATCCTGCGCAGCGT
mu: CATCCTGCACAGCGT		 TCCT|gcgc
Donor gained60740.31mu: TGCACAGCGTCAGCA CACA|gcgt
distance from splice site 60
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (Potential).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 756 / 756
chromosome 11
strand 1
last intron/exon boundary 740
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 879
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 680
gDNA position
(for ins/del: last normal base / first normal base)		 6072
chromosomal position
(for ins/del: last normal base / first normal base)		 61723364
original gDNA sequence snippet GGGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCT
altered gDNA sequence snippet GGGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCT
original cDNA sequence snippet GGGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCT
altered cDNA sequence snippet GGGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCT
wildtype AA sequence MEFQPNQEDE EDAHAGIIGR FLGLQSHDHH PPRANSRTKL LWPKRESLLH EGLPKNHKAA
KQNVRGQEDN KAWKLKAVDA FKSAPLYQRP GYYSAPQTPL SPTPMFFPLE PSAPSKLHSV
TGIDTKDKSL KTVSSGAKKS FELLSESDGA LMEHPEVSQV RRKTVEFNLT DMPEIPENHL
KEPLEQSPTN IHTTLKDHMD PYWALENRSV LHLNQGHCIA LCPTPASLAL SLPFLHNFLG
FHHCQSTLDL RPALAWGIYL ATFTGILGKC SGPFLTSPWY HPEDFLGPGE GR*
mutated AA sequence N/A
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