Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999685574 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>AN/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.25G>A
cDNA.138G>A
g.2011G>A
AA changes V9M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MTITYTSQVANARLGSFSRLL
mutated  all conserved    9 MTITYTSQMANARLGSFSRLLL
Ptroglodytes  all identical  ENSPTRG00000003756  9 MTITYTSQVANARLGSFSRLLL
Mmulatta  all identical  ENSMMUG00000015147  9 MTITYTSQVANARLGSFSRLLL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  all identical  ENSMUSG00000037418  9 MTITYTNKVANARLGSFSSLLL
Ggallus  all identical  ENSGALG00000007217  9 MTVTYTNRVADARLGTFSQLLL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  9 MTVTYSRRVADARLGTFYRLLL
Dmelanogaster  all identical  FBgn0040238  9 MTITYTGEVATCRGFGCFLKLLL
Celegans  all identical  C01B12.3  9 MTVTYSLDVASSSFFCLYKLLF
Xtropicalis  all identical  ENSXETG00000006740  9 MTVTYSNRVADARLGTFSRLLL
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).lost
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 25
cDNA position
(for ins/del: last normal base / first normal base)		 138
gDNA position
(for ins/del: last normal base / first normal base)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
original cDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered cDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 MTITYTSQMA 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 *
speed 0.91 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