Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999988537095 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM082491)
  • known disease mutation at this position (HGMD CM970096)
  • known disease mutation: rs18096 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:27264099T>CN/A show variant in all transcripts   IGV
HGNC symbol APP
Ensembl transcript ID ENST00000439274
Genbank transcript ID NM_001136130
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.1978A>G
cDNA.2012A>G
g.279348A>G
AA changes I660V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 660
frameshift no
known variant Reference ID: rs63750399
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs18096 (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 CM970096)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970096)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082491)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970096)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082491)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082491)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970096)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082491)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082491)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970096)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7451
4.7451
(flanking)2.821
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      660LMVGGVVIATVIVITLVMLKKKQY
mutated  all conserved    660LMVGGVVIATVVVITLVMLKKKQ
Ptroglodytes  all identical  ENSPTRG00000013811  716LMVGGVVIATVIVITLVMLKKKQ
Mmulatta  all identical  ENSMMUG00000014384  716LMVGGVVIATVIVITLVMLKKKQ
Fcatus  all identical  ENSFCAG00000001556  697LMVGGVVIATVIVITLVMLK
Mmusculus  all identical  ENSMUSG00000022892  641LMVGGVVIATVIVITLVMLKKKQ
Ggallus  all identical  ENSGALG00000015770  697LMVGGVVIATVIVITLVMLKKKQ
Trubripes  all identical  ENSTRUG00000010470  710LMVGGVVIATVIVITLVMLRKKQ
Drerio  all identical  ENSDARG00000055543  701LMVGGVVIATVIVITL
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  all identical  C42D8.8  633YVLASAMFITAICIIAFAITNAR
Xtropicalis  all identical  ENSXETG00000013612  717LMVGGVVIATVIVITLVMLKKKQ
protein features
start (aa)end (aa)featuredetails 
18699TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2145 / 2145
position (AA) of stopcodon in wt / mu AA sequence 715 / 715
position of stopcodon in wt / mu cDNA 2179 / 2179
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 2078
theoretical NMD boundary in CDS 1993
length of CDS 2145
coding sequence (CDS) position 1978
cDNA position
(for ins/del: last normal base / first normal base)		 2012
gDNA position
(for ins/del: last normal base / first normal base)		 279348
chromosomal position
(for ins/del: last normal base / first normal base)		 27264099
original gDNA sequence snippet GTGTTGTCATAGCGACAGTGATCGTCATCACCTTGGTGATG
altered gDNA sequence snippet GTGTTGTCATAGCGACAGTGGTCGTCATCACCTTGGTGATG
original cDNA sequence snippet GTGTTGTCATAGCGACAGTGATCGTCATCACCTTGGTGATG
altered cDNA sequence snippet GTGTTGTCATAGCGACAGTGGTCGTCATCACCTTGGTGATG
wildtype AA sequence MLPGLALLLL AAWTARALEV YPELQITNVV EANQPVTIQN WCKRGRKQCK THPHFVIPYR
CLVGEFVSDA LLVPDKCKFL HQERMDVCET HLHWHTVAKE TCSEKSTNLH DYGMLLPCGI
DKFRGVEFVC CPLAEESDNV DSADAEEDDS DVWWGGADTD YADGSEDKVV EVAEEEEVAE
VEEEEADDDE DDEDGDEVEE EAEEPYEEAT ERTTSIATTT TTTTESVEEV VREVCSEQAE
TGPCRAMISR WYFDVTEGKC APFFYGGCGG NRNNFDTEEY CMAVCGSAMS QSLLKTTQEP
LARDPVKLPT TAASTPDAVD KYLETPGDEN EHAHFQKAKE RLEAKHRERM SQVMREWEEA
ERQAKNLPKA DKKAVIQHFQ EKVESLEQEA ANERQQLVET HMARVEAMLN DRRRLALENY
ITALQAVPPR PRHVFNMLKK YVRAEQKDRQ HTLKHFEHVR MVDPKKAAQI RSQVMTHLRV
IYERMNQSLS LLYNVPAVAE EIQDEVDELL QKEQNYSDDV LANMISEPRI SYGNDALMPS
LTETKTTVEL LPVNGEFSLD DLQPWHSFGA DSVPANTENE VEPVDARPAA DRGLTTRPGS
GLTNIKTEEI SEVKMDAEFR HDSGYEVHHQ KLVFFAEDVG SNKGAIIGLM VGGVVIATVI
VITLVMLKKK QYTSIHHGVV EVDAAVTPEE RHLSKMQQNG YENPTYKFFE QMQN*
mutated AA sequence MLPGLALLLL AAWTARALEV YPELQITNVV EANQPVTIQN WCKRGRKQCK THPHFVIPYR
CLVGEFVSDA LLVPDKCKFL HQERMDVCET HLHWHTVAKE TCSEKSTNLH DYGMLLPCGI
DKFRGVEFVC CPLAEESDNV DSADAEEDDS DVWWGGADTD YADGSEDKVV EVAEEEEVAE
VEEEEADDDE DDEDGDEVEE EAEEPYEEAT ERTTSIATTT TTTTESVEEV VREVCSEQAE
TGPCRAMISR WYFDVTEGKC APFFYGGCGG NRNNFDTEEY CMAVCGSAMS QSLLKTTQEP
LARDPVKLPT TAASTPDAVD KYLETPGDEN EHAHFQKAKE RLEAKHRERM SQVMREWEEA
ERQAKNLPKA DKKAVIQHFQ EKVESLEQEA ANERQQLVET HMARVEAMLN DRRRLALENY
ITALQAVPPR PRHVFNMLKK YVRAEQKDRQ HTLKHFEHVR MVDPKKAAQI RSQVMTHLRV
IYERMNQSLS LLYNVPAVAE EIQDEVDELL QKEQNYSDDV LANMISEPRI SYGNDALMPS
LTETKTTVEL LPVNGEFSLD DLQPWHSFGA DSVPANTENE VEPVDARPAA DRGLTTRPGS
GLTNIKTEEI SEVKMDAEFR HDSGYEVHHQ KLVFFAEDVG SNKGAIIGLM VGGVVIATVV
VITLVMLKKK QYTSIHHGVV EVDAAVTPEE RHLSKMQQNG YENPTYKFFE QMQN*
speed 0.79 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