Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999991760805 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012047)
  • known disease mutation at this position (HGMD CM920017)
  • known disease mutation: rs13665 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887620G>CN/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.212G>C
cDNA.466G>C
g.51763G>C
AA changes R71P Score: 103 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
frameshift no
known variant Reference ID: rs121918003
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13665 (pathogenic for Infantile hypophosphatasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012047)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012047)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012047)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2341
5.2341
(flanking)-0.1380.987
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: 0.78wt: TGACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAAC
mu: TGACGGCTGCCCCCATCCTCAAGGGTCAGCTCCACCACAAC		 ctca|AGGG
Acc increased51772wt: 0.31 / mu: 0.63wt: GACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAACC
mu: GACGGCTGCCCCCATCCTCAAGGGTCAGCTCCACCACAACC		 tcaa|GGGT
Donor marginally increased51767wt: 0.9593 / mu: 0.9607 (marginal change - not scored)wt: CGCATCCTCAAGGGT
mu: CCCATCCTCAAGGGT		 CATC|ctca
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71DGMGVSTVTAARILKGQLHHNPGE
mutated  not conserved    71GMGVSTVTAAPILKGQLHHNPG
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 212
cDNA position
(for ins/del: last normal base / first normal base)		 466
gDNA position
(for ins/del: last normal base / first normal base)		 51763
chromosomal position
(for ins/del: last normal base / first normal base)		 21887620
original gDNA sequence snippet CTCCACAGTGACGGCTGCCCGCATCCTCAAGGGTCAGCTCC
altered gDNA sequence snippet CTCCACAGTGACGGCTGCCCCCATCCTCAAGGGTCAGCTCC
original cDNA sequence snippet CTCCACAGTGACGGCTGCCCGCATCCTCAAGGGTCAGCTCC
altered cDNA sequence snippet CTCCACAGTGACGGCTGCCCCCATCCTCAAGGGTCAGCTCC
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 PILKGQLHHN 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 1.56 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