Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999891338 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001382)
  • known disease mutation: rs2740 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61723364G>AN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000534553
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.104G>A
cDNA.680G>A
g.6072G>A
AA changes R35H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 35
frameshift no
known variant Reference ID: rs121918284
databasehomozygous (A/A)heterozygousallele carriers
1000G011
ExAC022

known disease mutation: rs2740 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|Vitreoretinochoroidopathy|Bestrophinopathy, autosomal recessive|Stargardt disease|Retinitis Pigmentosa, Recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001382)
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)5.8191
5.8191
(flanking)4.1861
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 increased6073wt: 0.4837 / mu: 0.4926 (marginal change - not scored)wt: GGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCTA
mu: GGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCTA		 gcgc|AGCG
Donor increased6076wt: 0.26 / mu: 0.53wt: CGCAGCGTCAGCACC
mu: CACAGCGTCAGCACC		 CAGC|gtca
Donor marginally increased6069wt: 0.8590 / mu: 0.8617 (marginal change - not scored)wt: CATCCTGCGCAGCGT
mu: CATCCTGCACAGCGT		 TCCT|gcgc
Donor gained60740.31mu: TGCACAGCGTCAGCA CACA|gcgt
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      35RYANLGNVLILRSVSTAVYKRFPS
mutated  not conserved    35RYANLGNVLILHSVSTAVYKRFP
Ptroglodytes  all identical  ENSPTRG00000003756  141RYANLGNVLILRSVSTAVYKRFP
Mmulatta  all identical  ENSMMUG00000015147  141RYANLGNVLILRSVSTAVYKRFP
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  all identical  ENSMUSG00000037418  141RYAILGQVLILRSISTSVYKRFP
Ggallus  all identical  ENSGALG00000007217  141RYSNLCSVLILRSVSTAVYKRFP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  141RYANLSGILIYRSVSTAVYKRFP
Dmelanogaster  not conserved  FBgn0040238  142RYVCLCLTMVLANVSPRVKKRFP
Celegans  all identical  C01B12.3  141RYSILTQAMVYRDVAASVRKRFP
Xtropicalis  all identical  ENSXETG00000006740  141RYANLTGLLILRSVSTAVYMRFP
protein features
start (aa)end (aa)featuredetails 
2646TRANSMEMHelical; (Potential).lost
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 168 / 168
position (AA) of stopcodon in wt / mu AA sequence 56 / 56
position of stopcodon in wt / mu cDNA 744 / 744
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 577 / 577
chromosome 11
strand 1
last intron/exon boundary 740
theoretical NMD boundary in CDS 113
length of CDS 168
coding sequence (CDS) position 104
cDNA position
(for ins/del: last normal base / first normal base)		 680
gDNA position
(for ins/del: last normal base / first normal base)		 6072
chromosomal position
(for ins/del: last normal base / first normal base)		 61723364
original gDNA sequence snippet GGGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCT
altered gDNA sequence snippet GGGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCT
original cDNA sequence snippet GGGCAACGTGCTCATCCTGCGCAGCGTCAGCACCGCAGTCT
altered cDNA sequence snippet GGGCAACGTGCTCATCCTGCACAGCGTCAGCACCGCAGTCT
wildtype AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAA*
mutated AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILHSVSTA VYKRFPSAQH LVQAA*
speed 0.56 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