Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998623993      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993515)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61723297G>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000378042
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.175G>C
cDNA.935G>C
g.6005G>C
AA changes E59Q Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 59
frameshift no
known variant Reference ID: rs1805142
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM993515)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993515)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993515)
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)0.0580.991
5.7691
(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
Donor marginally increased6005wt: 0.9054 / mu: 0.9406 (marginal change - not scored)wt: AGGACGAGCAAGGCC
mu: AGGACCAGCAAGGCC		 GACG|agca
Donor marginally increased6006wt: 0.9957 / mu: 0.9964 (marginal change - not scored)wt: GGACGAGCAAGGCCG
mu: GGACCAGCAAGGCCG		 ACGA|gcaa
Donor marginally increased5996wt: 0.9600 / mu: 0.9852 (marginal change - not scored)wt: TCGAAGGCAAGGACG
mu: TCGAAGGCAAGGACC		 GAAG|gcaa
Donor gained60100.40mu: CAGCAAGGCCGGCTG GCAA|ggcc
distance from splice site 108
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      59SLVSGFVEGKDEQGRLLRRTLIRY
mutated  all conserved    59SLVSGFVEGKDQQGRLLRRTLIR
Ptroglodytes  all identical  ENSPTRG00000003756  119SLVSGFVEGKDEQGRLLRRTLIR
Mmulatta  all identical  ENSMMUG00000015147  119SLVSGFVEGKDEQGRLLRRTLIR
Fcatus  not conserved  ENSFCAG00000007380  149XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000037418  119IQVSSFVEGKDEEGRLLRRTLIR
Ggallus  all identical  ENSGALG00000007217  119NLVSCNVDGEDEYGRLLRRTLMR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  119ALVSGHVRGADEGARLIRRSLMR
Dmelanogaster  all identical  FBgn0040238  120VFVSSNVHGQDERG
Celegans  all identical  C01B12.3  119LWITQYIKGETERA
Xtropicalis  all identical  ENSXETG00000006740  119CLVSSNVHGTDERG
protein features
start (aa)end (aa)featuredetails 
4770TOPO_DOMExtracellular (Potential).lost
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1497 / 1497
position (AA) of stopcodon in wt / mu AA sequence 499 / 499
position of stopcodon in wt / mu cDNA 2257 / 2257
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 761 / 761
chromosome 11
strand 1
last intron/exon boundary 2239
theoretical NMD boundary in CDS 1428
length of CDS 1497
coding sequence (CDS) position 175
cDNA position
(for ins/del: last normal base / first normal base)		 935
gDNA position
(for ins/del: last normal base / first normal base)		 6005
chromosomal position
(for ins/del: last normal base / first normal base)		 61723297
original gDNA sequence snippet GCTTCGTCGAAGGCAAGGACGAGCAAGGCCGGCTGCTGCGG
altered gDNA sequence snippet GCTTCGTCGAAGGCAAGGACCAGCAAGGCCGGCTGCTGCGG
original cDNA sequence snippet GCTTCGTCGAAGGCAAGGACGAGCAAGGCCGGCTGCTGCGG
altered cDNA sequence snippet GCTTCGTCGAAGGCAAGGACCAGCAAGGCCGGCTGCTGCGG
wildtype AA sequence MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*
mutated AA sequence MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDQQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*
speed 1.19 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