Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000439986
Querying Taster for transcript #2: ENST00000398179
MT speed 0 s - this script 2.365764 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CCBE1disease_causing_automatic0.999987956125999simple_aaeaffected0C75Ssingle base exchangers121908250show file
CCBE1disease_causing_automatic1without_aaeaffected0single base exchangers121908250show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999987956125999 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000439986
Genbank transcript ID NM_133459
UniProt peptide Q6UXH8
alteration type single base exchange
alteration region CDS
DNA changes c.223T>A
cDNA.261T>A
g.217153T>A
AA changes C75S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 75
frameshift no
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
effectgDNA positionscorewt detection sequence exon-intron border
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
Donor increased217148wt: 0.66 / mu: 0.99wt: GAAAAAGTGCTGCAA
mu: GAAAAAGTGCAGCAA		 AAAA|gtgc
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      75GELTTCYRKKCCKGYKFVLGQCIP
mutated  not conserved    75GELTTCYRKKCSKGYKFVLGQCI
Ptroglodytes  all identical  ENSPTRG00000010062  75GELTTCYRKKCCKGYKFVLGQCI
Mmulatta  all identical  ENSMMUG00000010402  75GELTTCYRKKCCKGYKFVLGQCI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046318  76GELTTCFRKKCCKGYKFVLGQCI
Ggallus  all identical  ENSGALG00000002613  6FRKKCCKGYKFVLGQCI
Trubripes  all identical  ENSTRUG00000012531  32GEAATCYRKKCCKGFKFVLGQCV
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021161  6FRKKCCKGYKFVLGQCI
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 223
cDNA position
(for ins/del: last normal base / first normal base)		 261
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 CATGCTACAGGAAAAAGTGCTGCAAAGGATATAAATTTGTT
altered cDNA sequence snippet CATGCTACAGGAAAAAGTGCAGCAAAGGATATAAATTTGTT
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 RKKCSKGYKF 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*
speed 0.13 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
back to results table
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 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
Donor increased217148wt: 0.66 / mu: 0.99wt: GAAAAAGTGCTGCAA
mu: GAAAAAGTGCAGCAA		 AAAA|gtgc
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 0.24 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
back to results table

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