Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.983352210913347 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>AN/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.781G>A
cDNA.942G>A
g.9706G>A
AA changes E261K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 261
frameshift no
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (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 CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      261LWWQSSSSTPLERMMMILRPTGLS
mutated  all conserved    261LWWQSSSSTPLKRMMMILRPTGL
Ptroglodytes  no alignment  ENSPTRG00000003756  n/a
Mmulatta  no alignment  ENSMMUG00000015147  n/a
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  no alignment  ENSMUSG00000037418  n/a
Ggallus  no alignment  ENSGALG00000007217  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000078331  n/a
Dmelanogaster  no alignment  FBgn0040238  n/a
Celegans  no alignment  C01B12.3  n/a
Xtropicalis  no alignment  ENSXETG00000006740  n/a
protein features
start (aa)end (aa)featuredetails 
250270TOPO_DOMExtracellular (Potential).lost
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 781
cDNA position
(for ins/del: last normal base / first normal base)		 942
gDNA position
(for ins/del: last normal base / first normal base)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
original cDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered cDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL KRMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
speed 1.09 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