Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999912156 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM044953)
  • known disease mutation: rs2746 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724929A>GN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000526988
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.389A>G
cDNA.550A>G
g.7637A>G
AA changes Y130C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 130
frameshift no
known variant Reference ID: rs121918291
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2746 (pathogenic for Vitreoretinochoroidopathy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM044953)

known disease mutation at this position, please check HGMD for details (HGMD ID CM044953)
known disease mutation at this position, please check HGMD for details (HGMD ID CM044953)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.9051
4.9051
(flanking)1.5891
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased7641wt: 0.21 / mu: 0.32wt: TATACACAGGTGAGG
mu: TGTACACAGGTGAGG		 TACA|cagg
Donor gained76310.79mu: CCCACTGGTGTGTAC CACT|ggtg
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      130YAYDWISIPLVYTQVVTVAVYSFF
mutated  not conserved    130YDWISIPLVCTQVVTVAVYSF
Ptroglodytes  all identical  ENSPTRG00000003756  236YDWISIPLVYTQVVTVAVYSF
Mmulatta  all identical  ENSMMUG00000015147  236YDWISIPLVYTQVVTVAVYSF
Fcatus  all identical  ENSFCAG00000007380  266FAYDWISIPLVYTQVVTVAVYSF
Mmusculus  all identical  ENSMUSG00000037418  236YDWISIPLVYTQVVTVAVYSF
Ggallus  all identical  ENSGALG00000007217  236YDWISIPLVYTQVVTVAVYSF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  236DWISLPLVYTQVVTVAVYSF
Dmelanogaster  all identical  FBgn0040238  240YDTISVPLVYTQVVTLAVYSY
Celegans  all identical  C01B12.3  236VPVPLVYTQVVHLAVRSY
Xtropicalis  all identical  ENSXETG00000006740  236YDWISVPLVYTQVVTVAVYSF
protein features
start (aa)end (aa)featuredetails 
92178TOPO_DOMCytoplasmic (Potential).lost
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 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1151 / 1151
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 162 / 162
chromosome 11
strand 1
last intron/exon boundary 1147
theoretical NMD boundary in CDS 935
length of CDS 990
coding sequence (CDS) position 389
cDNA position
(for ins/del: last normal base / first normal base)		 550
gDNA position
(for ins/del: last normal base / first normal base)		 7637
chromosomal position
(for ins/del: last normal base / first normal base)		 61724929
original gDNA sequence snippet GATTAGTATCCCACTGGTGTATACACAGGTGAGGACTAGGC
altered gDNA sequence snippet GATTAGTATCCCACTGGTGTGTACACAGGTGAGGACTAGGC
original cDNA sequence snippet GATTAGTATCCCACTGGTGTATACACAGGTGGTGACTGTGG
altered cDNA sequence snippet GATTAGTATCCCACTGGTGTGTACACAGGTGGTGACTGTGG
wildtype AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
mutated AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVC TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
speed 1.26 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