Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999993 (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
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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 ENST00000346798
Genbank transcript ID NM_000484
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.2150T>G
cDNA.2184T>G
g.279352T>G
AA changes V717G Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 717
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      717MVGGVVIATVIVITLVMLKKKQYT
mutated  not conserved    717MVGGVVIATVIGITL
Ptroglodytes  all identical  ENSPTRG00000013811  717MVGGVVIATVIVITL
Mmulatta  all identical  ENSMMUG00000014384  717MVGGVVIATVIVITL
Fcatus  all identical  ENSFCAG00000001556  698MVGGVVIATVIVITLVMLK
Mmusculus  all identical  ENSMUSG00000022892  642MVGGVVIATVIVITL
Ggallus  all identical  ENSGALG00000015770  698MVGGVVIATVIVITLVMLKKKQY
Trubripes  all identical  ENSTRUG00000010470  711MVGGVVIATVIVITLVM
Drerio  all identical  ENSDARG00000055543  698ATVIVITLVMLRKKQY
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  not conserved  C42D8.8  634VLASAMFITAICIIAFAITNARR
Xtropicalis  all identical  ENSXETG00000013612  718MVGGVVIATVIVIT
protein features
start (aa)end (aa)featuredetails 
700723TRANSMEMHelical; (Potential).lost
717717MUTAGENV->C,S: Unchanged beta-APP42/total APP- beta ratio.lost
717717MUTAGENV->F,G,I: Increased beta-APP42/beta-APP40 ratio.lost
717717MUTAGENV->K: Decreased beta-APP42/total APP-beta ratio.lost
717717MUTAGENV->M: Increased beta-APP42/beta-APP40 ratio. No change in apoptosis after caspase cleavage.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2313 / 2313
position (AA) of stopcodon in wt / mu AA sequence 771 / 771
position of stopcodon in wt / mu cDNA 2347 / 2347
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 35 / 35
chromosome 21
strand -1
last intron/exon boundary 2246
theoretical NMD boundary in CDS 2161
length of CDS 2313
coding sequence (CDS) position 2150
cDNA position
(for ins/del: last normal base / first normal base)		 2184
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 CGSAMSQSLL KTTQEPLARD
PVKLPTTAAS TPDAVDKYLE TPGDENEHAH FQKAKERLEA KHRERMSQVM REWEEAERQA
KNLPKADKKA VIQHFQEKVE SLEQEAANER QQLVETHMAR VEAMLNDRRR LALENYITAL
QAVPPRPRHV FNMLKKYVRA EQKDRQHTLK HFEHVRMVDP KKAAQIRSQV MTHLRVIYER
MNQSLSLLYN VPAVAEEIQD EVDELLQKEQ NYSDDVLANM ISEPRISYGN DALMPSLTET
KTTVELLPVN GEFSLDDLQP WHSFGADSVP ANTENEVEPV DARPAADRGL TTRPGSGLTN
IKTEEISEVK MDAEFRHDSG YEVHHQKLVF FAEDVGSNKG AIIGLMVGGV VIATVIVITL
VMLKKKQYTS IHHGVVEVDA AVTPEERHLS KMQQNGYENP TYKFFEQMQN *
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 CGSAMSQSLL KTTQEPLARD
PVKLPTTAAS TPDAVDKYLE TPGDENEHAH FQKAKERLEA KHRERMSQVM REWEEAERQA
KNLPKADKKA VIQHFQEKVE SLEQEAANER QQLVETHMAR VEAMLNDRRR LALENYITAL
QAVPPRPRHV FNMLKKYVRA EQKDRQHTLK HFEHVRMVDP KKAAQIRSQV MTHLRVIYER
MNQSLSLLYN VPAVAEEIQD EVDELLQKEQ NYSDDVLANM ISEPRISYGN DALMPSLTET
KTTVELLPVN GEFSLDDLQP WHSFGADSVP ANTENEVEPV DARPAADRGL TTRPGSGLTN
IKTEEISEVK MDAEFRHDSG YEVHHQKLVF FAEDVGSNKG AIIGLMVGGV VIATVIGITL
VMLKKKQYTS IHHGVVEVDA AVTPEERHLS KMQQNGYENP TYKFFEQMQN *
speed 1.41 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