Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999985857 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM000841)
  • known disease mutation at this position (HGMD CM1414063)
  • known disease mutation: rs2737 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61725631C>TN/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.548C>T
cDNA.634C>T
g.8339C>T
AA changes A183V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 183
frameshift no
known variant Reference ID: rs28940570
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2737 (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 CM000841)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000841)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1414063)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000841)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1414063)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000841)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7351
5.7351
(flanking)-5.1240
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8329wt: 0.5622 / mu: 0.5979 (marginal change - not scored)wt: CCTCCTCCTCCTCCCAGGTGGTGACTGTGGCGGTGTACAGC
mu: CCTCCTCCTCCTCCCAGGTGGTGACTGTGGTGGTGTACAGC		 gtgg|TGAC
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      183IPLVYTQVVTVAVYSFFLTCLVGR
mutated  not conserved    183TVVVYSFFLTCLVG
Ptroglodytes  all identical  ENSPTRG00000003756  243TVAVYSFFLTCLVG
Mmulatta  all identical  ENSMMUG00000015147  243TVAVYSFFLTCLVG
Fcatus  all identical  ENSFCAG00000007380  273TVAVYSFFLACLIG
Mmusculus  all identical  ENSMUSG00000037418  243TVAVYSFFLACLIG
Ggallus  all identical  ENSGALG00000007217  243TVAVYSFFLACLIG
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  243TVAVYSFFLTCLIG
Dmelanogaster  all identical  FBgn0040238  247VVTLAVYSYFLTCCMG
Celegans  all identical  C01B12.3  243LAVRSYFLIALFG
Xtropicalis  all identical  ENSXETG00000006740  243VAVYSFFLACLIG
protein features
start (aa)end (aa)featuredetails 
179199TRANSMEMHelical; (Potential).lost
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 548
cDNA position
(for ins/del: last normal base / first normal base)		 634
gDNA position
(for ins/del: last normal base / first normal base)		 8339
chromosomal position
(for ins/del: last normal base / first normal base)		 61725631
original gDNA sequence snippet CTCCCAGGTGGTGACTGTGGCGGTGTACAGCTTCTTCCTGA
altered gDNA sequence snippet CTCCCAGGTGGTGACTGTGGTGGTGTACAGCTTCTTCCTGA
original cDNA sequence snippet TACACAGGTGGTGACTGTGGCGGTGTACAGCTTCTTCCTGA
altered cDNA sequence snippet TACACAGGTGGTGACTGTGGTGGTGTACAGCTTCTTCCTGA
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
TVVVYSFFLT 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*
speed 0.87 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