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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 CM098496)
  • known disease mutation: rs446 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:57136800C>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.95G>C
g.227813G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121908251
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs446 (pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM098496)

known disease mutation at this position, please check HGMD for details (HGMD ID CM098496)
known disease mutation at this position, please check HGMD for details (HGMD ID CM098496)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4921
5.4911
(flanking)4.5471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -124) | splice site change before start ATG (at aa -122) | splice site change before start ATG (at aa -121) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased227804wt: 0.7112 / mu: 0.7247 (marginal change - not scored)wt: TTGTGCCGAGGCTCCCTGTGAACAGCAGTGCACGGACAACT
mu: TTGTGCCGAGGCTCCCTGTGAACAGCAGTCCACGGACAACT		 gtga|ACAG
Donor increased227811wt: 0.21 / mu: 0.46wt: CAGCAGTGCACGGAC
mu: CAGCAGTCCACGGAC		 GCAG|tgca
Donor increased227805wt: 0.70 / mu: 0.85wt: TGTGAACAGCAGTGC
mu: TGTGAACAGCAGTCC		 TGAA|cagc
Donor increased227815wt: 0.25 / mu: 0.42wt: AGTGCACGGACAACT
mu: AGTCCACGGACAACT		 TGCA|cgga
Donor marginally increased227817wt: 0.9082 / mu: 0.9309 (marginal change - not scored)wt: TGCACGGACAACTTT
mu: TCCACGGACAACTTT		 CACG|gaca
distance from splice site 40
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)		 95
gDNA position
(for ins/del: last normal base / first normal base)		 227813
chromosomal position
(for ins/del: last normal base / first normal base)		 57136800
original gDNA sequence snippet GGCTCCCTGTGAACAGCAGTGCACGGACAACTTTGGCCGAG
altered gDNA sequence snippet GGCTCCCTGTGAACAGCAGTCCACGGACAACTTTGGCCGAG
original cDNA sequence snippet GGCTCCCTGTGAACAGCAGTGCACGGACAACTTTGGCCGAG
altered cDNA sequence snippet GGCTCCCTGTGAACAGCAGTCCACGGACAACTTTGGCCGAG
wildtype AA sequence MQLTWASISL VTRCWPQTPT FQDLLACLGA RALPGPPGAP GRDGSKGERG APGPRGSPGP
PGSFDFLLLM LADIRNDITE LQEKVFGHRT HSSAEEFPLP QEFPSYPEAM DLGSGDDHPR
RTETRDLRAP RDFYP*
mutated AA sequence N/A
speed 0.81 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