Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999877 (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 ENST00000448388
Genbank transcript ID NM_001136131
UniProt peptide P05067
alteration type single base exchange
alteration region CDS
DNA changes c.1820T>G
cDNA.2012T>G
g.279352T>G
AA changes V607G Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 607
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      607MVGGVVIATVIVITLVMLKKKQYT
mutated  not conserved    607VIATVIGITLVMLKKKQY
Ptroglodytes  all identical  ENSPTRG00000013811  717MVGGVVIATVIVITLVMLKKKQY
Mmulatta  all identical  ENSMMUG00000014384  717MVGGVVIATVIVITLVMLKKKQY
Fcatus  all identical  ENSFCAG00000001556  698MVGGVVIATVIVITLVMLK
Mmusculus  all identical  ENSMUSG00000022892  642VIATVIVITLVMLKKKQY
Ggallus  all identical  ENSGALG00000015770  698ATVIVITLVMLKKKQY
Trubripes  all identical  ENSTRUG00000010470  711MVGGVVIATVIVITLVMLRKKQY
Drerio  all identical  ENSDARG00000055543  698MVGGVVIATVIVITLVMLRKKQY
Dmelanogaster  no alignment  FBgn0000108  n/a
Celegans  not conserved  C42D8.8  635TAICIIAFAITNARR
Xtropicalis  all identical  ENSXETG00000013612  718MVGGVVIATVIVITLVMLKKKQY
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 1983 / 1983
position (AA) of stopcodon in wt / mu AA sequence 661 / 661
position of stopcodon in wt / mu cDNA 2175 / 2175
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 193 / 193
chromosome 21
strand -1
last intron/exon boundary 2074
theoretical NMD boundary in CDS 1831
length of CDS 1983
coding sequence (CDS) position 1820
cDNA position
(for ins/del: last normal base / first normal base)		 2012
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 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 VVRVPTTAAS 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 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 VVRVPTTAAS 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 1.17 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