Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999983 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910039)
  • known disease mutation: rs18090 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:27264095A>CN/A show variant in all transcripts   IGV
HGNC symbol APP
Ensembl transcript ID ENST00000357903
Genbank transcript ID NM_201413
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.2093T>G
cDNA.2260T>G
g.279352T>G
AA changes V698G Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 698
frameshift no
known variant Reference ID: rs63749964
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18090 (pathogenic for Alzheimer disease, type 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910039)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910039)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910039)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.9561
4.7451
(flanking)5.7321
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased279344wt: 0.7349 / mu: 0.7902 (marginal change - not scored)wt: GCGACAGTGATCGTC
mu: GCGACAGTGATCGGC		 GACA|gtga
distance from splice site 62
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      698MVGGVVIATVIVITLVMLKKKQYT
mutated  not conserved    698MVGGVVIATVIGITLVMLKKKQY
Ptroglodytes  all identical  ENSPTRG00000013811  717MVGGVVIATVIVITL
Mmulatta  all identical  ENSMMUG00000014384  717MVGGVVIATVIVITL
Fcatus  all identical  ENSFCAG00000001556  698MVGGVVIATVIVITLVMLK
Mmusculus  all identical  ENSMUSG00000022892  642MVGGVVIATVIVITLVMLKKKQY
Ggallus  all identical  ENSGALG00000015770  698MVGGVVIATVIVITLVMLKKKQY
Trubripes  all identical  ENSTRUG00000010470  711MVGGVVIATVIVITLVM
Drerio  all identical  ENSDARG00000055543  698MVGGVVIATVIVITLVMLRKKQY
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  not conserved  C42D8.8  635VLASAMFITAICIIAFAITNARR
Xtropicalis  all identical  ENSXETG00000013612  718MVGGVVIATVIVIT
protein features
start (aa)end (aa)featuredetails 
18699TOPO_DOMExtracellular (Potential).lost
688711PEPTIDEP3(40). /FTId=PRO_0000000096.lost
688713PEPTIDEP3(42). /FTId=PRO_0000000095.lost
698700STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2256 / 2256
position (AA) of stopcodon in wt / mu AA sequence 752 / 752
position of stopcodon in wt / mu cDNA 2423 / 2423
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 168 / 168
chromosome 21
strand -1
last intron/exon boundary 2322
theoretical NMD boundary in CDS 2104
length of CDS 2256
coding sequence (CDS) position 2093
cDNA position
(for ins/del: last normal base / first normal base)		 2260
gDNA position
(for ins/del: last normal base / first normal base)		 279352
chromosomal position
(for ins/del: last normal base / first normal base)		 27264095
original gDNA sequence snippet TGTCATAGCGACAGTGATCGTCATCACCTTGGTGATGCTGA
altered gDNA sequence snippet TGTCATAGCGACAGTGATCGGCATCACCTTGGTGATGCTGA
original cDNA sequence snippet TGTCATAGCGACAGTGATCGTCATCACCTTGGTGATGCTGA
altered cDNA sequence snippet TGTCATAGCGACAGTGATCGGCATCACCTTGGTGATGCTGA
wildtype AA sequence MLPGLALLLL AAWTARALEV PTDGNAGLLA EPQIAMFCGR LNMHMNVQNG KWDSDPSGTK
TCIDTKEGIL QYCQEVYPEL QITNVVEANQ PVTIQNWCKR GRKQCKTHPH FVIPYRCLVG
EFVSDALLVP DKCKFLHQER MDVCETHLHW HTVAKETCSE KSTNLHDYGM LLPCGIDKFR
GVEFVCCPLA EESDNVDSAD AEEDDSDVWW GGADTDYADG SEDKVVEVAE EEEVAEVEEE
EADDDEDDED GDEVEEEAEE PYEEATERTT SIATTTTTTT ESVEEVVREV CSEQAETGPC
RAMISRWYFD VTEGKCAPFF YGGCGGNRNN FDTEEYCMAV CGSAIPTTAA STPDAVDKYL
ETPGDENEHA HFQKAKERLE AKHRERMSQV MREWEEAERQ AKNLPKADKK AVIQHFQEKV
ESLEQEAANE RQQLVETHMA RVEAMLNDRR RLALENYITA LQAVPPRPRH VFNMLKKYVR
AEQKDRQHTL KHFEHVRMVD PKKAAQIRSQ VMTHLRVIYE RMNQSLSLLY NVPAVAEEIQ
DEVDELLQKE QNYSDDVLAN MISEPRISYG NDALMPSLTE TKTTVELLPV NGEFSLDDLQ
PWHSFGADSV PANTENEVEP VDARPAADRG LTTRPGSGLT NIKTEEISEV KMDAEFRHDS
GYEVHHQKLV FFAEDVGSNK GAIIGLMVGG VVIATVIVIT LVMLKKKQYT SIHHGVVEVD
AAVTPEERHL SKMQQNGYEN PTYKFFEQMQ N*
mutated AA sequence MLPGLALLLL AAWTARALEV PTDGNAGLLA EPQIAMFCGR LNMHMNVQNG KWDSDPSGTK
TCIDTKEGIL QYCQEVYPEL QITNVVEANQ PVTIQNWCKR GRKQCKTHPH FVIPYRCLVG
EFVSDALLVP DKCKFLHQER MDVCETHLHW HTVAKETCSE KSTNLHDYGM LLPCGIDKFR
GVEFVCCPLA EESDNVDSAD AEEDDSDVWW GGADTDYADG SEDKVVEVAE EEEVAEVEEE
EADDDEDDED GDEVEEEAEE PYEEATERTT SIATTTTTTT ESVEEVVREV CSEQAETGPC
RAMISRWYFD VTEGKCAPFF YGGCGGNRNN FDTEEYCMAV CGSAIPTTAA STPDAVDKYL
ETPGDENEHA HFQKAKERLE AKHRERMSQV MREWEEAERQ AKNLPKADKK AVIQHFQEKV
ESLEQEAANE RQQLVETHMA RVEAMLNDRR RLALENYITA LQAVPPRPRH VFNMLKKYVR
AEQKDRQHTL KHFEHVRMVD PKKAAQIRSQ VMTHLRVIYE RMNQSLSLLY NVPAVAEEIQ
DEVDELLQKE QNYSDDVLAN MISEPRISYG NDALMPSLTE TKTTVELLPV NGEFSLDDLQ
PWHSFGADSV PANTENEVEP VDARPAADRG LTTRPGSGLT NIKTEEISEV KMDAEFRHDS
GYEVHHQKLV FFAEDVGSNK GAIIGLMVGG VVIATVIGIT LVMLKKKQYT SIHHGVVEVD
AAVTPEERHL SKMQQNGYEN PTYKFFEQMQ N*
speed 0.92 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