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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000252486
MT speed 0 s - this script 2.777953 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APOEdisease_causing_automatic0.987967094538819simple_aaeaffected0R43Csingle base exchangers121918399show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.987967094538819 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993912)
  • known disease mutation: rs17880 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45411100C>TN/A show variant in all transcripts   IGV
HGNC symbol APOE
Ensembl transcript ID ENST00000252486
Genbank transcript ID NM_000041
UniProt peptide P02649
alteration type single base exchange
alteration region CDS
DNA changes c.127C>T
cDNA.238C>T
g.2090C>T
AA changes R43C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 43
frameshift no
known variant Reference ID: rs121918399
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs17880 (pathogenic for Lipoprotein glomerulopathy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993912)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993912)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993912)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2760.973
1.1170.995
(flanking)2.0941
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2083wt: 0.64 / mu: 0.97wt: CAGAGCGGCCAGCGC
mu: CAGAGCGGCCAGTGC		 GAGC|ggcc
Donor marginally increased2093wt: 0.3575 / mu: 0.4335 (marginal change - not scored)wt: AGCGCTGGGAACTGG
mu: AGTGCTGGGAACTGG		 CGCT|ggga
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      43LRQQTEWQSGQRWELALGRFWDYL
mutated  not conserved    43LRQQTEWQSGQCWELALGRFWDY
Ptroglodytes  all identical  ENSPTRG00000011127  43LHHLAEWQSGQRWELALGHFWDY
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000002985  43VTDQLEWQSNQPWEQALNRFWDY
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000000934  57-----------HWQGVVNRFWQY
Drerio  all identical  ENSDARG00000040295  43-----------RWEEMVDRFWQY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000019317  46-----------KWETALDSFWLT
protein features
start (aa)end (aa)featuredetails 
4042TURNmight get lost (downstream of altered splice site)
4360HELIXlost
6370HELIXmight get lost (downstream of altered splice site)
7396HELIXmight get lost (downstream of altered splice site)
80101REPEAT1.might get lost (downstream of altered splice site)
80255REGION8 X 22 AA approximate tandem repeats.might get lost (downstream of altered splice site)
9393CARBOHYDN-linked (Glc) (glycation).might get lost (downstream of altered splice site)
9799TURNmight get lost (downstream of altered splice site)
102123REPEAT2.might get lost (downstream of altered splice site)
106141HELIXmight get lost (downstream of altered splice site)
124145REPEAT3.might get lost (downstream of altered splice site)
143145TURNmight get lost (downstream of altered splice site)
146167REPEAT4.might get lost (downstream of altered splice site)
147147MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
149179HELIXmight get lost (downstream of altered splice site)
158168REGIONLDL receptor binding (Potential).might get lost (downstream of altered splice site)
162165REGIONHeparin-binding.might get lost (downstream of altered splice site)
168189REPEAT5.might get lost (downstream of altered splice site)
180182TURNmight get lost (downstream of altered splice site)
187190TURNmight get lost (downstream of altered splice site)
190211REPEAT6.might get lost (downstream of altered splice site)
193198HELIXmight get lost (downstream of altered splice site)
200202STRANDmight get lost (downstream of altered splice site)
209217HELIXmight get lost (downstream of altered splice site)
212212CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
212233REPEAT7.might get lost (downstream of altered splice site)
228241HELIXmight get lost (downstream of altered splice site)
229236REGIONHeparin-binding.might get lost (downstream of altered splice site)
234255REPEAT8.might get lost (downstream of altered splice site)
257283HELIXmight get lost (downstream of altered splice site)
286303HELIXmight get lost (downstream of altered splice site)
307307CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
307309STRANDmight get lost (downstream of altered splice site)
308308CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 954 / 954
position (AA) of stopcodon in wt / mu AA sequence 318 / 318
position of stopcodon in wt / mu cDNA 1065 / 1065
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 112 / 112
chromosome 19
strand 1
last intron/exon boundary 348
theoretical NMD boundary in CDS 186
length of CDS 954
coding sequence (CDS) position 127
cDNA position
(for ins/del: last normal base / first normal base)		 238
gDNA position
(for ins/del: last normal base / first normal base)		 2090
chromosomal position
(for ins/del: last normal base / first normal base)		 45411100
original gDNA sequence snippet CCGAGTGGCAGAGCGGCCAGCGCTGGGAACTGGCACTGGGT
altered gDNA sequence snippet CCGAGTGGCAGAGCGGCCAGTGCTGGGAACTGGCACTGGGT
original cDNA sequence snippet CCGAGTGGCAGAGCGGCCAGCGCTGGGAACTGGCACTGGGT
altered cDNA sequence snippet CCGAGTGGCAGAGCGGCCAGTGCTGGGAACTGGCACTGGGT
wildtype AA sequence MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQRWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*
mutated AA sequence MKVLWAALLV TFLAGCQAKV EQAVETEPEP ELRQQTEWQS GQCWELALGR FWDYLRWVQT
LSEQVQEELL SSQVTQELRA LMDETMKELK AYKSELEEQL TPVAEETRAR LSKELQAAQA
RLGADMEDVC GRLVQYRGEV QAMLGQSTEE LRVRLASHLR KLRKRLLRDA DDLQKRLAVY
QAGAREGAER GLSAIRERLG PLVEQGRVRA ATVGSLAGQP LQERAQAWGE RLRARMEEMG
SRTRDRLDEV KEQVAEVRAK LEEQAQQIRL QAEAFQARLK SWFEPLVEDM QRQWAGLVEK
VQAAVGTSAA PVPSDNH*
speed 0.77 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
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