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 3.611328 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CCBE1disease_causing_automatic0.999999982451567simple_aae0G56Rsingle base exchangers121908252show file
CCBE1disease_causing_automatic0.999999989432464simple_aae0G327Rsingle base exchangers121908252show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999982451567 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM098497)
  • known disease mutation: rs447 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:57105351C>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 CDS
DNA changes c.166G>C
cDNA.629G>C
g.259262G>C
AA changes G56R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 56
frameshift no
known variant Reference ID: rs121908252
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs447 (pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)

known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)
known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3171
5.3171
(flanking)-0.2470.522
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      56SKGERGAPGPRGSPGPPGSFDFLL
mutated  not conserved    56SKGERGAPGPRRSPGP
Ptroglodytes  all identical  ENSPTRG00000010062  327SKGERGAPGPRGSPGPPGSFDFL
Mmulatta  all identical  ENSMMUG00000010402  327SKGERGAPGPRGSPGPPGSFDFL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046318  329SKGERGAPGPPGSPGPPGSFDFL
Ggallus  all identical  ENSGALG00000002613  259SKGERGAPGPKGIPGPPGSFDFL
Trubripes  all identical  ENSTRUG00000012531  280LKGDRGAPGPAGLPGPPGSFDFL
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021161  248TKGDRGAPGPRGPPGPPGSFDFL
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 408 / 408
position (AA) of stopcodon in wt / mu AA sequence 136 / 136
position of stopcodon in wt / mu cDNA 871 / 871
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 166
cDNA position
(for ins/del: last normal base / first normal base)		 629
gDNA position
(for ins/del: last normal base / first normal base)		 259262
chromosomal position
(for ins/del: last normal base / first normal base)		 57105351
original gDNA sequence snippet GAGGAGCGCCTGGGCCCAGAGGGTCTCCAGTAAGTAGCACT
altered gDNA sequence snippet GAGGAGCGCCTGGGCCCAGACGGTCTCCAGTAAGTAGCACT
original cDNA sequence snippet GAGGAGCGCCTGGGCCCAGAGGGTCTCCAGGACCCCCTGGT
altered cDNA sequence snippet GAGGAGCGCCTGGGCCCAGACGGTCTCCAGGACCCCCTGGT
wildtype AA sequence MQLTWASISL VTRCWPQTPT FQDLLACLGA RALPGPPGAP GRDGSKGERG APGPRGSPGP
PGSFDFLLLM LADIRNDITE LQEKVFGHRT HSSAEEFPLP QEFPSYPEAM DLGSGDDHPR
RTETRDLRAP RDFYP*
mutated AA sequence MQLTWASISL VTRCWPQTPT FQDLLACLGA RALPGPPGAP GRDGSKGERG APGPRRSPGP
PGSFDFLLLM LADIRNDITE LQEKVFGHRT HSSAEEFPLP QEFPSYPEAM DLGSGDDHPR
RTETRDLRAP RDFYP*
speed 0.87 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: simple_aae, prob: 0.999999989432464 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM098497)
  • known disease mutation: rs447 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr18:57105351C>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.979G>C
cDNA.1017G>C
g.259262G>C
AA changes G327R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 327
frameshift no
known variant Reference ID: rs121908252
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs447 (pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)

known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)
known disease mutation at this position, please check HGMD for details (HGMD ID CM098497)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3171
5.3171
(flanking)-0.2470.522
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      327SKGERGAPGPRGSPGPPGSFDFLL
mutated  not conserved    327SKGERGAPGPRRSPGPPGSFDFL
Ptroglodytes  all identical  ENSPTRG00000010062  327SKGERGAPGPRGSPGPPGSFDFL
Mmulatta  all identical  ENSMMUG00000010402  327SKGERGAPGPRGSPGPPGSFDFL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046318  329SKGERGAPGPPGSPGPPGSFDFL
Ggallus  all identical  ENSGALG00000002613  259SKGERGAPGPKGIPGPPGSFDFL
Trubripes  all identical  ENSTRUG00000012531  280LKGDRGAPGPAGLPGPPGSFDFL
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021161  248TKGDRGAPGPRGPPGPPGSFDFL
protein features
start (aa)end (aa)featuredetails 
300333DOMAINCollagen-like 2.lost
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 979
cDNA position
(for ins/del: last normal base / first normal base)		 1017
gDNA position
(for ins/del: last normal base / first normal base)		 259262
chromosomal position
(for ins/del: last normal base / first normal base)		 57105351
original gDNA sequence snippet GAGGAGCGCCTGGGCCCAGAGGGTCTCCAGTAAGTAGCACT
altered gDNA sequence snippet GAGGAGCGCCTGGGCCCAGACGGTCTCCAGTAAGTAGCACT
original cDNA sequence snippet GAGGAGCGCCTGGGCCCAGAGGGTCTCCAGGACCCCCTGGT
altered cDNA sequence snippet GAGGAGCGCCTGGGCCCAGACGGTCTCCAGGACCCCCTGGT
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 QCTDNFGRVL CTCYPGYRYD
RERHRKREKP YCLDIDECAS SNGTLCAHIC INTLGSYRCE CREGYIREDD GKTCTRGDKY
PNDTGHEKSE NMVKAGTCCA TCKEFYQMKQ TVLQLKQKIA LLPNNAADLG KYITGDKVLA
SNTYLPGPPG LPGGQGPPGS PGPKGSPGFP GMPGPPGQPG PRGSMGPMGP SPDLSHIKQG
RRGPVGPPGA PGRDGSKGER GAPGPRRSPG PPGSFDFLLL MLADIRNDIT ELQEKVFGHR
THSSAEEFPL PQEFPSYPEA MDLGSGDDHP RRTETRDLRA PRDFYP*
speed 0.75 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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