Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999966326 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080107)
  • known disease mutation: rs2742 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61727364G>AN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000449131
Genbank transcript ID NM_001139443
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.769G>A
cDNA.855G>A
g.10072G>A
AA changes V257M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 257
frameshift no
known variant Reference ID: rs121918287
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2742 (pathogenic for Bestrophinopathy, autosomal recessive) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080107)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7121
5.7121
(flanking)4.7171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost10071sequence motif lost- wt: ccag|GTGT
 mu: ccag.ATGT
Acc marginally increased10083wt: 0.5601 / mu: 0.5851 (marginal change - not scored)wt: GGTGACCAGGTGTCCCTGTTGGCTGTGGATGAGATGCACCA
mu: GGTGACCAGATGTCCCTGTTGGCTGTGGATGAGATGCACCA		 gttg|GCTG
Acc marginally increased10062wt: 0.9015 / mu: 0.9032 (marginal change - not scored)wt: TGTGGGACTTCTTCTGTCCCTGGTGACCAGGTGTCCCTGTT
mu: TGTGGGACTTCTTCTGTCCCTGGTGACCAGATGTCCCTGTT		 ccct|GGTG
Donor gained100680.89mu: GGTGACCAGATGTCC TGAC|caga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      257ETNWIVDRNLQVSLLAVDEMHQDL
mutated  all conserved    257ETNWIVDRNLQMSLLAVDEMHQD
Ptroglodytes  all identical  ENSPTRG00000003756  317ETNWIVDRNLQVSLLAVDEMHQD
Mmulatta  all identical  ENSMMUG00000015147  317ETNWIVDRNLQVSLLAVDEMHQD
Fcatus  all identical  ENSFCAG00000007380  347ETNWIVDRSLQVSLLAVDEMHQD
Mmusculus  all identical  ENSMUSG00000037418  317ETNWIIDRNLQVSLLSVDGMHQN
Ggallus  all identical  ENSGALG00000007217  317ETNWLIDRNLQVSLMAVDEMHQD
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  317ETNWLVDRNLQVSLLSVDEMYDL
Dmelanogaster  all identical  FBgn0040238  324EVNWMVDRNLQVSYLIVDEMHHD
Celegans  all identical  C01B12.3  320ECNWILDRNLQVGLMVVDTAYNR
Xtropicalis  all identical  ENSXETG00000006740  317ETNWLIDRNLQVSLLAVDEMHQD
protein features
start (aa)end (aa)featuredetails 
250270TOPO_DOMExtracellular (Potential).lost
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 1815 / 1815
position (AA) of stopcodon in wt / mu AA sequence 605 / 605
position of stopcodon in wt / mu cDNA 1901 / 1901
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 87 / 87
chromosome 11
strand 1
last intron/exon boundary 1007
theoretical NMD boundary in CDS 870
length of CDS 1815
coding sequence (CDS) position 769
cDNA position
(for ins/del: last normal base / first normal base)		 855
gDNA position
(for ins/del: last normal base / first normal base)		 10072
chromosomal position
(for ins/del: last normal base / first normal base)		 61727364
original gDNA sequence snippet CTTCTGTCCCTGGTGACCAGGTGTCCCTGTTGGCTGTGGAT
altered gDNA sequence snippet CTTCTGTCCCTGGTGACCAGATGTCCCTGTTGGCTGTGGAT
original cDNA sequence snippet TTGTCGACAGGAATTTGCAGGTGTCCCTGTTGGCTGTGGAT
altered cDNA sequence snippet TTGTCGACAGGAATTTGCAGATGTCCCTGTTGGCTGTGGAT
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 AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*
mutated 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 AEQLINPFGE
DDDDFETNWI VDRNLQMSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*
speed 0.50 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