Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995041998 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000435278
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.253T>C
cDNA.366T>C
g.5903T>C
AA changes Y85H Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 85
frameshift no
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
effectgDNA positionscorewt detection 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? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85QLIPISFVLGFYVTLVVTRWWNQY
mutated  all conserved    85QLIPISFVLGFHVTLVVTRWWNQ
Ptroglodytes  all identical  ENSPTRG00000003756  85QLIPISFVLGFYVTLVVTRWWNQ
Mmulatta  all identical  ENSMMUG00000015147  85QLIPISFVLGFYVTLVVTRWWNQ
Fcatus  not conserved  ENSFCAG00000007380  115QLIPISFVLXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000037418  85QLIPISFVLGFYVTLVVSRWWSQ
Ggallus  all identical  ENSGALG00000007217  85ELIPVSFVLGFYVSLVVSRWWAQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  85QLIPVSFVLGFYVTLVVSRWWGQ
Dmelanogaster  all identical  FBgn0040238  86ELIPLSFVLGFYVSIVMTRWWNQ
Celegans  all identical  C01B12.3  85NFIPITFMLGFYVSAVFTRWWQI
Xtropicalis  all identical  ENSXETG00000006740  85ELIPVSFVLGFYVTLVVSRWWGQ
protein features
start (aa)end (aa)featuredetails 
7191TRANSMEMHelical; (Potential).lost
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 926 / 926
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 114 / 114
chromosome 11
strand 1
last intron/exon boundary 828
theoretical NMD boundary in CDS 664
length of CDS 813
coding sequence (CDS) position 253
cDNA position
(for ins/del: last normal base / first normal base)		 366
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 TTTCCTTCGTGCTGGGCTTCTACGTGACGCTGGTCGTGACC
altered cDNA sequence snippet TTTCCTTCGTGCTGGGCTTCCACGTGACGCTGGTCGTGACC
wildtype AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
mutated AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFHVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
speed 1.11 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