Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999922 (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 ENST00000440126
Genbank transcript ID NM_001136016
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.2078T>G
cDNA.2235T>G
g.279352T>G
AA changes V693G Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 693
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      693MVGGVVIATVIVITLVMLKKKQYT
mutated  not conserved    693MVGGVVIATVIGITLVMLKKKQY
Ptroglodytes  all identical  ENSPTRG00000013811  717MVGGVVIATVIVITLVMLKKKQY
Mmulatta  all identical  ENSMMUG00000014384  717MVGGVVIATVIVITLVMLKKKQY
Fcatus  all identical  ENSFCAG00000001556  698MVGGVVIATVIVITLVMLK
Mmusculus  all identical  ENSMUSG00000022892  642MVGGVVIATVIVITLVMLKKKQY
Ggallus  all identical  ENSGALG00000015770  698MVGGVVIATVIVITLVMLKKKQY
Trubripes  all identical  ENSTRUG00000010470  711MVGGVVIATVIVITLVMLRKKQY
Drerio  all identical  ENSDARG00000055543  698MVGGVVIATVIVITLVMLRKKQY
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  not conserved  C42D8.8  635VLASAMFITAICIIAFAITNARR
Xtropicalis  all identical  ENSXETG00000013612  718MVGGVVIATVIVITLVMLKKKQY
protein features
start (aa)end (aa)featuredetails 
18699TOPO_DOMExtracellular (Potential).lost
688711PEPTIDEP3(40). /FTId=PRO_0000000096.lost
688713PEPTIDEP3(42). /FTId=PRO_0000000095.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2241 / 2241
position (AA) of stopcodon in wt / mu AA sequence 747 / 747
position of stopcodon in wt / mu cDNA 2398 / 2398
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 158 / 158
chromosome 21
strand -1
last intron/exon boundary 2297
theoretical NMD boundary in CDS 2089
length of CDS 2241
coding sequence (CDS) position 2078
cDNA position
(for ins/del: last normal base / first normal base)		 2235
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 MDQLEDLLVL FINYVPTDGN AGLLAEPQIA MFCGRLNMHM NVQNGKWDSD PSGTKTCIDT
KEGILQYCQE VYPELQITNV VEANQPVTIQ NWCKRGRKQC KTHPHFVIPY RCLVGEFVSD
ALLVPDKCKF LHQERMDVCE THLHWHTVAK ETCSEKSTNL HDYGMLLPCG IDKFRGVEFV
CCPLAEESDN VDSADAEEDD SDVWWGGADT DYADGSEDKV VEVAEEEEVA EVEEEEADDD
EDDEDGDEVE EEAEEPYEEA TERTTSIATT TTTTTESVEE VVREVCSEQA ETGPCRAMIS
RWYFDVTEGK CAPFFYGGCG GNRNNFDTEE YCMAVCGSAI PTTAASTPDA VDKYLETPGD
ENEHAHFQKA KERLEAKHRE RMSQVMREWE EAERQAKNLP KADKKAVIQH FQEKVESLEQ
EAANERQQLV ETHMARVEAM LNDRRRLALE NYITALQAVP PRPRHVFNML KKYVRAEQKD
RQHTLKHFEH VRMVDPKKAA QIRSQVMTHL RVIYERMNQS LSLLYNVPAV AEEIQDEVDE
LLQKEQNYSD DVLANMISEP RISYGNDALM PSLTETKTTV ELLPVNGEFS LDDLQPWHSF
GADSVPANTE NEVEPVDARP AADRGLTTRP GSGLTNIKTE EISEVKMDAE FRHDSGYEVH
HQKLVFFAED VGSNKGAIIG LMVGGVVIAT VIVITLVMLK KKQYTSIHHG VVEVDAAVTP
EERHLSKMQQ NGYENPTYKF FEQMQN*
mutated AA sequence MDQLEDLLVL FINYVPTDGN AGLLAEPQIA MFCGRLNMHM NVQNGKWDSD PSGTKTCIDT
KEGILQYCQE VYPELQITNV VEANQPVTIQ NWCKRGRKQC KTHPHFVIPY RCLVGEFVSD
ALLVPDKCKF LHQERMDVCE THLHWHTVAK ETCSEKSTNL HDYGMLLPCG IDKFRGVEFV
CCPLAEESDN VDSADAEEDD SDVWWGGADT DYADGSEDKV VEVAEEEEVA EVEEEEADDD
EDDEDGDEVE EEAEEPYEEA TERTTSIATT TTTTTESVEE VVREVCSEQA ETGPCRAMIS
RWYFDVTEGK CAPFFYGGCG GNRNNFDTEE YCMAVCGSAI PTTAASTPDA VDKYLETPGD
ENEHAHFQKA KERLEAKHRE RMSQVMREWE EAERQAKNLP KADKKAVIQH FQEKVESLEQ
EAANERQQLV ETHMARVEAM LNDRRRLALE NYITALQAVP PRPRHVFNML KKYVRAEQKD
RQHTLKHFEH VRMVDPKKAA QIRSQVMTHL RVIYERMNQS LSLLYNVPAV AEEIQDEVDE
LLQKEQNYSD DVLANMISEP RISYGNDALM PSLTETKTTV ELLPVNGEFS LDDLQPWHSF
GADSVPANTE NEVEPVDARP AADRGLTTRP GSGLTNIKTE EISEVKMDAE FRHDSGYEVH
HQKLVFFAED VGSNKGAIIG LMVGGVVIAT VIGITLVMLK KKQYTSIHHG VVEVDAAVTP
EERHLSKMQQ NGYENPTYKF FEQMQN*
speed 1.17 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