Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999724187591 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM880005)
  • known disease mutation: rs13662 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21890596G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374840
Genbank transcript ID NM_000478
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.535G>A
cDNA.785G>A
g.54739G>A
AA changes A179T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 179
frameshift no
known variant Reference ID: rs121918000
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13662 (pathogenic for Infantile hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM880005)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880005)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880005)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.140.24
5.2341
(flanking)3.6371
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 increased54740wt: 0.4021 / mu: 0.4167 (marginal change - not scored)wt: CACCCCCAGCGCCGCCTACGCCCACTCGGCTGACCGGGACT
mu: CACCCCCAGCGCCGCCTACACCCACTCGGCTGACCGGGACT		 acgc|CCAC
distance from splice site 63
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      179RVNHATPSAAYAHSADRDWYSDNE
mutated  not conserved    179RVNHATPSAAYTHSADRDWYSDN
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  179RVNHATPSAAYAHSADRDWYSDN
Fcatus  all identical  ENSFCAG00000002960  179RVNHATPSAAYAHSADRDWYSDN
Mmusculus  all identical  ENSMUSG00000028766  179RVNHATPSAAYAHSADRDWYSDN
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  180RVNHATPSASYAHSVDRDWLSDS
Drerio  all identical  ENSDARG00000015546  216RVNHATPSAAYAHCV
Dmelanogaster  all identical  FBgn0043791  214SVTHASPAGVYAHLANRNWENDA
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1825 / 1825
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 251 / 251
chromosome 1
strand 1
last intron/exon boundary 1560
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 535
cDNA position
(for ins/del: last normal base / first normal base)		 785
gDNA position
(for ins/del: last normal base / first normal base)		 54739
chromosomal position
(for ins/del: last normal base / first normal base)		 21890596
original gDNA sequence snippet CCACCCCCAGCGCCGCCTACGCCCACTCGGCTGACCGGGAC
altered gDNA sequence snippet CCACCCCCAGCGCCGCCTACACCCACTCGGCTGACCGGGAC
original cDNA sequence snippet CCACCCCCAGCGCCGCCTACGCCCACTCGGCTGACCGGGAC
altered cDNA sequence snippet CCACCCCCAGCGCCGCCTACACCCACTCGGCTGACCGGGAC
wildtype AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
mutated AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYTH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 1.22 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