Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999924843      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs13663 (probable pathogenic)
  • known disease mutation at this position (HGMD CM172367)
  • known disease mutation at this position (HGMD CM920018)
  • known disease mutation at this position (HGMD CM921023)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887619C>TN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374832
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.211C>T
cDNA.465C>T
g.51762C>T
AA changes R71C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
frameshift no
known variant Reference ID: rs121918001
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs13663 (probable pathogenic for Infantile hypophosphatasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.20.998
5.2341
(flanking)5.2341
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased51771wt: 0.47 / mu: 0.58wt: TGACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAAC
mu: TGACGGCTGCCTGCATCCTCAAGGGTCAGCTCCACCACAAC		 ctca|AGGG
Acc increased51772wt: 0.31 / mu: 0.38wt: GACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAACC
mu: GACGGCTGCCTGCATCCTCAAGGGTCAGCTCCACCACAACC		 tcaa|GGGT
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71DGMGVSTVTAARILKGQLHHNPGE
mutated  not conserved    71GMGVSTVTAACILKGQLHHNPG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  71GMGVSTVTATRILKGQLHHNPG
Fcatus  all identical  ENSFCAG00000002960  71GMGVSTVTAARILKGQLHHNPG
Mmusculus  all identical  ENSMUSG00000028766  71GMGVSTVTAARILKGQLHHNTG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  72DGMGVPTVTAARILKGQLSGQSG
Drerio  all identical  ENSDARG00000015546  108GVPTVTAARILKGQLSGQNG
Dmelanogaster  all identical  FBgn0043791  111DGMSIPTITAGRVYLG--
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
104104CONFLICTN -> K (in Ref. 3; CAA32376).might get lost (downstream of altered splice site)
110110ACT_SITEPhosphoserine intermediate.might get lost (downstream of altered splice site)
140140CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
173173METALMagnesium (Potential).might get lost (downstream of altered splice site)
230230CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
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 1829 / 1829
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 255 / 255
chromosome 1
strand 1
last intron/exon boundary 1564
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 211
cDNA position
(for ins/del: last normal base / first normal base)		 465
gDNA position
(for ins/del: last normal base / first normal base)		 51762
chromosomal position
(for ins/del: last normal base / first normal base)		 21887619
original gDNA sequence snippet TCTCCACAGTGACGGCTGCCCGCATCCTCAAGGGTCAGCTC
altered gDNA sequence snippet TCTCCACAGTGACGGCTGCCTGCATCCTCAAGGGTCAGCTC
original cDNA sequence snippet TCTCCACAGTGACGGCTGCCCGCATCCTCAAGGGTCAGCTC
altered cDNA sequence snippet TCTCCACAGTGACGGCTGCCTGCATCCTCAAGGGTCAGCTC
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 CILKGQLHHN 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*
speed 0.81 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