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 CM098495)
  • known disease mutation: rs445 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:57147460A>TN/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.13T>A
g.217153T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908250
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs445 (pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM098495)

known disease mutation at this position, please check HGMD for details (HGMD ID CM098495)
known disease mutation at this position, please check HGMD for details (HGMD ID CM098495)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.7381
3.1221
(flanking)3.7381
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -150) | splice site change before start ATG (at aa -147) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased217148wt: 0.66 / mu: 0.99wt: GAAAAAGTGCTGCAA
mu: GAAAAAGTGCAGCAA		 AAAA|gtgc
Donor increased217158wt: 0.27 / mu: 0.49wt: TGCAAAGGATATAAA
mu: AGCAAAGGATATAAA		 CAAA|ggat
Donor marginally increased217153wt: 0.9980 / mu: 0.9991 (marginal change - not scored)wt: AGTGCTGCAAAGGAT
mu: AGTGCAGCAAAGGAT		 TGCT|gcaa
distance from splice site 13
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)		 13
gDNA position
(for ins/del: last normal base / first normal base)		 217153
chromosomal position
(for ins/del: last normal base / first normal base)		 57147460
original gDNA sequence snippet TGTCTCTTAGGAAAAAGTGCTGCAAAGGATATAAATTTGTT
altered gDNA sequence snippet TGTCTCTTAGGAAAAAGTGCAGCAAAGGATATAAATTTGTT
original cDNA sequence snippet AGGAAAAAGTGCTGCAAAGGATATAAATTTGTT
altered cDNA sequence snippet AGGAAAAAGTGCAGCAAAGGATATAAATTTGTT
wildtype AA sequence MQLTWASISL VTRCWPQTPT FQDLLACLGA RALPGPPGAP GRDGSKGERG APGPRGSPGP
PGSFDFLLLM LADIRNDITE LQEKVFGHRT HSSAEEFPLP QEFPSYPEAM DLGSGDDHPR
RTETRDLRAP RDFYP*
mutated AA sequence N/A
speed 0.57 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