Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM098499)
  • known disease mutation: rs450 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:57134004A>GN/A show variant in all transcripts   IGV
HGNC symbol CCBE1
Ensembl transcript ID ENST00000398179
Genbank transcript ID N/A
UniProt peptide Q6UXH8
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.310T>C
g.230609T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908254
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs450 (pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM098499)

known disease mutation at this position, please check HGMD for details (HGMD ID CM098499)
known disease mutation at this position, please check HGMD for details (HGMD ID CM098499)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5321
4.2190.997
(flanking)-1.6730.267
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -50) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor marginally increased230604wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TGGGAAGACATGTAC
mu: TGGGAAGACACGTAC		 GGAA|gaca
Donor gained2306080.35mu: AAGACACGTACCAGG GACA|cgta
distance from splice site 34
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
134SIGNALPotential.might get lost (downstream of altered splice site)
134175DOMAINEGF-like; calcium-binding (Potential).might get lost (downstream of altered splice site)
138138DISULFIDBy similarity.might get lost (downstream of altered splice site)
142142CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
146146DISULFIDBy similarity.might get lost (downstream of altered splice site)
150150DISULFIDBy similarity.might get lost (downstream of altered splice site)
159159DISULFIDBy similarity.might get lost (downstream of altered splice site)
161161DISULFIDBy similarity.might get lost (downstream of altered splice site)
174174DISULFIDBy similarity.might get lost (downstream of altered splice site)
182182CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
245290DOMAINCollagen-like 1.might get lost (downstream of altered splice site)
300333DOMAINCollagen-like 2.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 464 / 464
chromosome 18
strand -1
last intron/exon boundary 638
theoretical NMD boundary in CDS 124
length of CDS 408
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 310
gDNA position
(for ins/del: last normal base / first normal base)		 230609
chromosomal position
(for ins/del: last normal base / first normal base)		 57134004
original gDNA sequence snippet GGGAAGATGATGGGAAGACATGTACCAGGGGAGACAAATAT
altered gDNA sequence snippet GGGAAGATGATGGGAAGACACGTACCAGGGGAGACAAATAT
original cDNA sequence snippet GGGAAGATGATGGGAAGACATGTACCAGGGGAGACAAATAT
altered cDNA sequence snippet GGGAAGATGATGGGAAGACACGTACCAGGGGAGACAAATAT
wildtype AA sequence MQLTWASISL VTRCWPQTPT FQDLLACLGA RALPGPPGAP GRDGSKGERG APGPRGSPGP
PGSFDFLLLM LADIRNDITE LQEKVFGHRT HSSAEEFPLP QEFPSYPEAM DLGSGDDHPR
RTETRDLRAP RDFYP*
mutated AA sequence N/A
speed 0.54 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