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: ENST00000227667
Querying Taster for transcript #2: ENST00000375345
MT speed 0 s - this script 4.163673 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APOC3disease_causing_automatic1.04581291321082e-11simple_aae0K78Esingle base exchangers121918382show file
APOC3disease_causing_automatic1.04581291321082e-11simple_aae0K96Esingle base exchangers121918382show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 1.04581291321082e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910037)
  • known disease mutation: rs17903 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116703532A>GN/A show variant in all transcripts   IGV
HGNC symbol APOC3
Ensembl transcript ID ENST00000227667
Genbank transcript ID NM_000040
UniProt peptide P02656
alteration type single base exchange
alteration region CDS
DNA changes c.232A>G
cDNA.294A>G
g.3111A>G
AA changes K78E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 78
frameshift no
known variant Reference ID: rs121918382
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs17903 (pathogenic for Hyperalphalipoproteinemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.9430
0.2350
(flanking)-1.0880
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 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78FSSLKDYWSTVKDKFSEFWDLDPE
mutated  all conserved    78FSSLKDYWSTVEDKFSEFWDLDP
Ptroglodytes  all identical  ENSPTRG00000004315  96FSSLKDYWSTVKDKFSEFWDSDP
Mmulatta  all identical  ENSMMUG00000016126  78FSSLKDYWSTVKDKLSGFWDLNP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000032081  116FRSLKGYWSKFTDKFTGFWDSNP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
6899REGIONLipid-binding.lost
6980HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 300 / 300
position (AA) of stopcodon in wt / mu AA sequence 100 / 100
position of stopcodon in wt / mu cDNA 362 / 362
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 63 / 63
chromosome 11
strand 1
last intron/exon boundary 242
theoretical NMD boundary in CDS 129
length of CDS 300
coding sequence (CDS) position 232
cDNA position
(for ins/del: last normal base / first normal base)		 294
gDNA position
(for ins/del: last normal base / first normal base)		 3111
chromosomal position
(for ins/del: last normal base / first normal base)		 116703532
original gDNA sequence snippet AAGACTACTGGAGCACCGTTAAGGACAAGTTCTCTGAGTTC
altered gDNA sequence snippet AAGACTACTGGAGCACCGTTGAGGACAAGTTCTCTGAGTTC
original cDNA sequence snippet AAGACTACTGGAGCACCGTTAAGGACAAGTTCTCTGAGTTC
altered cDNA sequence snippet AAGACTACTGGAGCACCGTTGAGGACAAGTTCTCTGAGTTC
wildtype AA sequence MQPRVLLVVA LLALLASARA SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR
GWVTDGFSSL KDYWSTVKDK FSEFWDLDPE VRPTSAVAA*
mutated AA sequence MQPRVLLVVA LLALLASARA SEAEDASLLS FMQGYMKHAT KTAKDALSSV QESQVAQQAR
GWVTDGFSSL KDYWSTVEDK FSEFWDLDPE VRPTSAVAA*
speed 1.29 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: 1.04581291321082e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910037)
  • known disease mutation: rs17903 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:116703532A>GN/A show variant in all transcripts   IGV
HGNC symbol APOC3
Ensembl transcript ID ENST00000375345
Genbank transcript ID N/A
UniProt peptide P02656
alteration type single base exchange
alteration region CDS
DNA changes c.286A>G
cDNA.348A>G
g.3111A>G
AA changes K96E Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 96
frameshift no
known variant Reference ID: rs121918382
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs17903 (pathogenic for Hyperalphalipoproteinemia 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910037)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.9430
0.2350
(flanking)-1.0880
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 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      96FSSLKDYWSTVKDKFSEFWDLDPE
mutated  all conserved    96FSSLKDYWSTVEDKFSEFWDLDP
Ptroglodytes  all identical  ENSPTRG00000004315  96FSSLKDYWSTVKDKFSEFWDSDP
Mmulatta  all identical  ENSMMUG00000016126  78FSSLKDYWSTVKDKLSGFWDLNP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000032081  116FRSLKGYWSKFTDKFTGFWDSNP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
6899REGIONLipid-binding.lost
9398HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 354 / 354
position (AA) of stopcodon in wt / mu AA sequence 118 / 118
position of stopcodon in wt / mu cDNA 416 / 416
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 63 / 63
chromosome 11
strand 1
last intron/exon boundary 296
theoretical NMD boundary in CDS 183
length of CDS 354
coding sequence (CDS) position 286
cDNA position
(for ins/del: last normal base / first normal base)		 348
gDNA position
(for ins/del: last normal base / first normal base)		 3111
chromosomal position
(for ins/del: last normal base / first normal base)		 116703532
original gDNA sequence snippet AAGACTACTGGAGCACCGTTAAGGACAAGTTCTCTGAGTTC
altered gDNA sequence snippet AAGACTACTGGAGCACCGTTGAGGACAAGTTCTCTGAGTTC
original cDNA sequence snippet AAGACTACTGGAGCACCGTTAAGGACAAGTTCTCTGAGTTC
altered cDNA sequence snippet AAGACTACTGGAGCACCGTTGAGGACAAGTTCTCTGAGTTC
wildtype AA sequence MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVKDKFS EFWDLDPEVR PTSAVAA*
mutated AA sequence MGTWGAPHRT LPCRNRGAMQ PRVLLVVALL ALLASARASE AEDASLLSFM QGYMKHATKT
AKDALSSVQE SQVAQQARGW VTDGFSSLKD YWSTVEDKFS EFWDLDPEVR PTSAVAA*
speed 0.91 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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