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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 CM982020)
  • known disease mutation: rs2728 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61723195T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000534553
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.511T>C
g.5903T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940274
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2728 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982020)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982020)
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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7721
4.7631
(flanking)4.7631
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -22) | splice site change before start ATG (at aa -21) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased5904wt: 0.33 / mu: 0.36wt: CCCCTCCTGCCCAGGCTTCTACGTGACGCTGGTCGTGACCC
mu: CCCCTCCTGCCCAGGCTTCCACGTGACGCTGGTCGTGACCC		 tcta|CGTG
Acc marginally increased5895wt: 0.8375 / mu: 0.8636 (marginal change - not scored)wt: CGCCCCCCGCCCCTCCTGCCCAGGCTTCTACGTGACGCTGG
mu: CGCCCCCCGCCCCTCCTGCCCAGGCTTCCACGTGACGCTGG		 gccc|AGGC
Acc marginally increased5896wt: 0.8747 / mu: 0.8894 (marginal change - not scored)wt: GCCCCCCGCCCCTCCTGCCCAGGCTTCTACGTGACGCTGGT
mu: GCCCCCCGCCCCTCCTGCCCAGGCTTCCACGTGACGCTGGT		 ccca|GGCT
Donor increased5900wt: 0.42 / mu: 0.66wt: CAGGCTTCTACGTGA
mu: CAGGCTTCCACGTGA		 GGCT|tcta
distance from splice site 6
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 577 / 577
chromosome 11
strand 1
last intron/exon boundary 740
theoretical NMD boundary in CDS 113
length of CDS 168
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 511
gDNA position
(for ins/del: last normal base / first normal base)		 5903
chromosomal position
(for ins/del: last normal base / first normal base)		 61723195
original gDNA sequence snippet GCCCCTCCTGCCCAGGCTTCTACGTGACGCTGGTCGTGACC
altered gDNA sequence snippet GCCCCTCCTGCCCAGGCTTCCACGTGACGCTGGTCGTGACC
original cDNA sequence snippet GAAGTTAGACGTTAGGCTTCTACGTGACGCTGGTCGTGACC
altered cDNA sequence snippet GAAGTTAGACGTTAGGCTTCCACGTGACGCTGGTCGTGACC
wildtype AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAA*
mutated AA sequence N/A
speed 0.97 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