Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999966908061 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000439986
Genbank transcript ID NM_133459
UniProt peptide Q6UXH8
alteration type single base exchange
alteration region CDS
DNA changes c.305G>C
cDNA.343G>C
g.227813G>C
AA changes C102S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 102
frameshift no
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
effectgDNA positionscorewt detection 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? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      102DVCAEAPCEQQCTDNFGRVLCTCY
mutated  not conserved    102DVCAEAPCEQQSTDNFGRVLCTC
Ptroglodytes  all identical  ENSPTRG00000010062  102DVCAEAPCEQQCTDNFGRVLCTC
Mmulatta  all identical  ENSMMUG00000010402  102DVCAEAPCEQQCTDNFGRVLCTC
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046318  103DICAQAPCEQQCTDNFGRVLCTC
Ggallus  all identical  ENSGALG00000002613  33DVCAEAPCEQQCTDNFGRVLCTC
Trubripes  all identical  ENSTRUG00000012531  59DVCTDAPCEQQCTDHFGRVVCTC
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021161  33DVCSEAPCEQQCTDNFGM-----
protein features
start (aa)end (aa)featuredetails 
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1221 / 1221
position (AA) of stopcodon in wt / mu AA sequence 407 / 407
position of stopcodon in wt / mu cDNA 1259 / 1259
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 39 / 39
chromosome 18
strand -1
last intron/exon boundary 1026
theoretical NMD boundary in CDS 937
length of CDS 1221
coding sequence (CDS) position 305
cDNA position
(for ins/del: last normal base / first normal base)		 343
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 MVPPPPSRGG AARGQLGRSL GPLLLLLALG HTWTYREEPE DGDREICSES KIATTKYPCL
KSSGELTTCY RKKCCKGYKF VLGQCIPEDY DVCAEAPCEQ QCTDNFGRVL CTCYPGYRYD
RERHRKREKP YCLDIDECAS SNGTLCAHIC INTLGSYRCE CREGYIREDD GKTCTRGDKY
PNDTGHEKSE NMVKAGTCCA TCKEFYQMKQ TVLQLKQKIA LLPNNAADLG KYITGDKVLA
SNTYLPGPPG LPGGQGPPGS PGPKGSPGFP GMPGPPGQPG PRGSMGPMGP SPDLSHIKQG
RRGPVGPPGA PGRDGSKGER GAPGPRGSPG PPGSFDFLLL MLADIRNDIT ELQEKVFGHR
THSSAEEFPL PQEFPSYPEA MDLGSGDDHP RRTETRDLRA PRDFYP*
mutated AA sequence MVPPPPSRGG AARGQLGRSL GPLLLLLALG HTWTYREEPE DGDREICSES KIATTKYPCL
KSSGELTTCY RKKCCKGYKF VLGQCIPEDY DVCAEAPCEQ QSTDNFGRVL CTCYPGYRYD
RERHRKREKP YCLDIDECAS SNGTLCAHIC INTLGSYRCE CREGYIREDD GKTCTRGDKY
PNDTGHEKSE NMVKAGTCCA TCKEFYQMKQ TVLQLKQKIA LLPNNAADLG KYITGDKVLA
SNTYLPGPPG LPGGQGPPGS PGPKGSPGFP GMPGPPGQPG PRGSMGPMGP SPDLSHIKQG
RRGPVGPPGA PGRDGSKGER GAPGPRGSPG PPGSFDFLLL MLADIRNDIT ELQEKVFGHR
THSSAEEFPL PQEFPSYPEA MDLGSGDDHP RRTETRDLRA PRDFYP*
speed 1.10 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