Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 3.66510069254309e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000435278
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.122T>C
cDNA.235T>C
g.2108T>C
AA changes L41P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 41
frameshift no
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
Acc marginally increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41KLLYGEFLIFLLCYYIIRFIYRLA
mutated  not conserved    41KLLYGEFLIFLPCYYIIRFIYRL
Ptroglodytes  all identical  ENSPTRG00000003756  41KLLYGEFLIFLLCYYIIRFIYRL
Mmulatta  all identical  ENSMMUG00000015147  41KLLYGEFFIFLLCYYIIRFIYRL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  not conserved  ENSMUSG00000037418  41KLLYGEFLVFIFLYYSIRGLYRM
Ggallus  not conserved  ENSGALG00000007217  41KLLYSEFLIFISLYFAISLVYRL
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000078331  41KLLYRELLIFTVMYCIISITYRC
Dmelanogaster  not conserved  FBgn0040238  41KLVWLDLLAFLTIYYAINMVYRF
Celegans  not conserved  C01B12.3  41KSVWAELVVWLCLYAVLSVIYRC
Xtropicalis  not conserved  ENSXETG00000006740  41KLLYREFLIFISCYFIISVTYRF
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 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 926 / 926
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 114 / 114
chromosome 11
strand 1
last intron/exon boundary 828
theoretical NMD boundary in CDS 664
length of CDS 813
coding sequence (CDS) position 122
cDNA position
(for ins/del: last normal base / first normal base)		 235
gDNA position
(for ins/del: last normal base / first normal base)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered cDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
wildtype AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
mutated AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL PCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
speed 1.24 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