Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999895880794 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM011910)
  • known disease mutation: rs18101 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:27264165C>TN/A show variant in all transcripts   IGV
HGNC symbol APP
Ensembl transcript ID ENST00000358918
Genbank transcript ID NM_001204301
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.2026G>A
cDNA.2226G>A
g.279282G>A
AA changes D676N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 676
frameshift no
known variant Reference ID: rs63749810
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18101 (pathogenic for Alzheimer disease|ABeta amyloidosis, Iowa type|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM011910)

known disease mutation at this position, please check HGMD for details (HGMD ID CM011910)
known disease mutation at this position, please check HGMD for details (HGMD ID CM011910)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7451
4.0531
(flanking)2.2681
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased279277wt: 0.5630 / mu: 0.6058 (marginal change - not scored)wt: TGTTTTCAAGGTGTTCTTTGCAGAAGATGTGGGTTCAAACA
mu: TGTTTTCAAGGTGTTCTTTGCAGAAAATGTGGGTTCAAACA		 ttgc|AGAA
Acc increased279279wt: 0.62 / mu: 0.77wt: TTTTCAAGGTGTTCTTTGCAGAAGATGTGGGTTCAAACAAA
mu: TTTTCAAGGTGTTCTTTGCAGAAAATGTGGGTTCAAACAAA		 gcag|AAGA
Donor marginally increased279279wt: 0.6197 / mu: 0.6806 (marginal change - not scored)wt: TTGCAGAAGATGTGG
mu: TTGCAGAAAATGTGG		 GCAG|aaga
Donor gained2792770.56mu: CTTTGCAGAAAATGT TTGC|agaa
Donor gained2792780.58mu: TTTGCAGAAAATGTG TGCA|gaaa
distance from splice site 16
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      676VHHQKLVFFAEDVGSNKGAIIGLM
mutated  all conserved    676VHHQKLVFFAENVGSNKGAIIGL
Ptroglodytes  all identical  ENSPTRG00000013811  694VHHQKLVFFAEDVGSNKGAIIGL
Mmulatta  all identical  ENSMMUG00000014384  694VHHQKLVFFAEDVGSNKGAIIGL
Fcatus  all identical  ENSFCAG00000001556  675VHHQKLVFFAEDVGSNKGAIIGL
Mmusculus  all identical  ENSMUSG00000022892  619VRHQKLVFFAEDVGSNKGAIIGL
Ggallus  all identical  ENSGALG00000015770  675VHHQKLVFFAEDVGSNKGAIIGL
Trubripes  all identical  ENSTRUG00000010470  688VHHQKLVFFAEDVGSNKGAIIGL
Drerio  all identical  ENSDARG00000055543  674VRDKRLMFLAEDMGSNKGAIIGL
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  not conserved  C42D8.8  611FYRHDKLIQSPEVERSASSVFQPY
Xtropicalis  all conserved  ENSXETG00000013612  695VHHQKLVFFAEEVGSNKGAIIGL
protein features
start (aa)end (aa)featuredetails 
18699TOPO_DOMExtracellular (Potential).lost
674677TURNlost
676676MUTAGENR->G: 60-70% zinc-induced beta-APP (28) peptide aggregation.lost
677677METALCopper or zinc 2.might get lost (downstream of altered splice site)
679679CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
679682STRANDmight get lost (downstream of altered splice site)
681681METALCopper or zinc 2 (Probable).might get lost (downstream of altered splice site)
681681MUTAGENY->F: 60-70% zinc-induced beta-APP (28) peptide aggregation.might get lost (downstream of altered splice site)
683685STRANDmight get lost (downstream of altered splice site)
684684METALCopper or zinc 2.might get lost (downstream of altered splice site)
684684MUTAGENH->R: Only 23% zinc-induced beta-APP (28) peptide aggregation.might get lost (downstream of altered splice site)
685685METALCopper or zinc 2.might get lost (downstream of altered splice site)
687688SITECleavage; by alpha-secretase.might get lost (downstream of altered splice site)
688691STRANDmight get lost (downstream of altered splice site)
688711PEPTIDEP3(40). /FTId=PRO_0000000096.might get lost (downstream of altered splice site)
688713PEPTIDEP3(42). /FTId=PRO_0000000095.might get lost (downstream of altered splice site)
690691SITECleavage; by theta-secretase.might get lost (downstream of altered splice site)
695697HELIXmight get lost (downstream of altered splice site)
697697CARBOHYDO-linked (GalNAc...).might get lost (downstream of altered splice site)
698700STRANDmight get lost (downstream of altered splice site)
700723TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
702705STRANDmight get lost (downstream of altered splice site)
704704SITEImplicated in free radical propagation (By similarity).might get lost (downstream of altered splice site)
704704MUTAGENG->V: Reduced protein oxidation. No hippocampal neuron toxicity.might get lost (downstream of altered splice site)
706706SITESusceptible to oxidation.might get lost (downstream of altered splice site)
706706MUTAGENM->L: Reduced lipid peroxidation inhibition.might get lost (downstream of altered splice site)
706706MUTAGENM->V: No free radical production. No hippocampal neuron toxicity.might get lost (downstream of altered splice site)
707712STRANDmight get lost (downstream of altered splice site)
711712SITECleavage; by gamma-secretase; site 1.might get lost (downstream of altered splice site)
713714SITECleavage; by gamma-secretase; site 2.might get lost (downstream of altered splice site)
717717MUTAGENV->K: Decreased beta-APP42/total APP-beta ratio.might get lost (downstream of altered splice site)
717717MUTAGENV->M: Increased beta-APP42/beta-APP40 ratio. No change in apoptosis after caspase cleavage.might get lost (downstream of altered splice site)
717717MUTAGENV->C,S: Unchanged beta-APP42/total APP- beta ratio.might get lost (downstream of altered splice site)
717717MUTAGENV->F,G,I: Increased beta-APP42/beta-APP40 ratio.might get lost (downstream of altered splice site)
720721SITECleavage; by gamma-secretase; site 3.might get lost (downstream of altered splice site)
724724CONFLICTMissing (in Ref. 22; AAB26263/AAB26264).might get lost (downstream of altered splice site)
724734MOTIFBasolateral sorting signal.might get lost (downstream of altered splice site)
724770TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
728728MUTAGENY->A: No effect on APBA1 nor APBB1 binding. Greatly reduces the binding to APPBP2. APP internalization unchanged. No change in beta-APP42 secretion.might get lost (downstream of altered splice site)
729729MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
730730MOD_RESPhosphoserine; by APP-kinase I (By similarity).might get lost (downstream of altered splice site)
731731CONFLICTI -> N (in Ref. 22; AAB26263/AAB26264/ AAB26265).might get lost (downstream of altered splice site)
732751REGIONInteraction with G(o)-alpha.might get lost (downstream of altered splice site)
739739MUTAGEND->N: No effect on FADD-induced apoptosis.might get lost (downstream of altered splice site)
739739MUTAGEND->A: No cleavage by caspases during apoptosis.might get lost (downstream of altered splice site)
739740SITECleavage; by caspase-6, caspase-8 or caspase-9.might get lost (downstream of altered splice site)
743743MUTAGENT->A: Greatly reduces the binding to SHC1 and APBB family members; no effect on NGF-stimulated neurite extension.might get lost (downstream of altered splice site)
743743MOD_RESPhosphothreonine; by CDK5 and MAPK10.might get lost (downstream of altered splice site)
743743MUTAGENT->E: Reduced NGF-stimulated neurite extension. No effect on APP maturation.might get lost (downstream of altered splice site)
744754HELIXmight get lost (downstream of altered splice site)
755758STRANDmight get lost (downstream of altered splice site)
756756MUTAGENG->A: APP internalization unchanged. No change in beta-APP42 secretion.might get lost (downstream of altered splice site)
757757CONFLICTY -> S (in Ref. 30; AAA35540).might get lost (downstream of altered splice site)
757757MUTAGENY->A: Little APP internalization. Reduced beta-APP42 secretion.might get lost (downstream of altered splice site)
757757MUTAGENY->G: Loss of binding to MAPK8IP1, APBA1, APBB1, APPBP2 and SHC1.might get lost (downstream of altered splice site)
757757MOD_RESPhosphotyrosine; by ABL1 (By similarity).might get lost (downstream of altered splice site)
757757MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
759759MUTAGENN->A: No binding to APBA1, no effect on APBB1 binding. Little APP internalization. Reduced beta-APP42 secretion.might get lost (downstream of altered splice site)
759762MOTIFNPXY motif; contains endocytosis signal.might get lost (downstream of altered splice site)
760760MUTAGENP->A: Little APP internalization. Reduced beta-APP42 secretion.might get lost (downstream of altered splice site)
762762MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
762762MUTAGENY->A: Loss of binding to APBA1 and APBB1. APP internalization unchanged. No change in beta-APP42 secretion.might get lost (downstream of altered splice site)
763765STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2259 / 2259
position (AA) of stopcodon in wt / mu AA sequence 753 / 753
position of stopcodon in wt / mu cDNA 2459 / 2459
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 201 / 201
chromosome 21
strand -1
last intron/exon boundary 2358
theoretical NMD boundary in CDS 2107
length of CDS 2259
coding sequence (CDS) position 2026
cDNA position
(for ins/del: last normal base / first normal base)		 2226
gDNA position
(for ins/del: last normal base / first normal base)		 279282
chromosomal position
(for ins/del: last normal base / first normal base)		 27264165
original gDNA sequence snippet TCAAGGTGTTCTTTGCAGAAGATGTGGGTTCAAACAAAGGT
altered gDNA sequence snippet TCAAGGTGTTCTTTGCAGAAAATGTGGGTTCAAACAAAGGT
original cDNA sequence snippet AATTGGTGTTCTTTGCAGAAGATGTGGGTTCAAACAAAGGT
altered cDNA sequence snippet AATTGGTGTTCTTTGCAGAAAATGTGGGTTCAAACAAAGGT
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 ANTENEGSGL TNIKTEEISE VKMDAEFRHD
SGYEVHHQKL VFFAEDVGSN KGAIIGLMVG GVVIATVIVI TLVMLKKKQY TSIHHGVVEV
DAAVTPEERH LSKMQQNGYE NPTYKFFEQM QN*
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 ANTENEGSGL TNIKTEEISE VKMDAEFRHD
SGYEVHHQKL VFFAENVGSN KGAIIGLMVG GVVIATVIVI TLVMLKKKQY TSIHHGVVEV
DAAVTPEERH LSKMQQNGYE NPTYKFFEQM QN*
speed 0.58 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