Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99992009838204 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM920019)
  • known disease mutation: rs13670 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21890632G>AN/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.571G>A
cDNA.825G>A
g.54775G>A
AA changes E191K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 191
frameshift no
known variant Reference ID: rs121918007
databasehomozygous (A/A)heterozygousallele carriers
1000G044
ExAC1310311

known disease mutation: rs13670 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Odontohypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920019)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920019)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2980.721
5.1741
(flanking)2.7351
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 increased54772wt: 0.2065 / mu: 0.2167 (marginal change - not scored)wt: CAGACAACGAGATGC
mu: CAGACAACAAGATGC		 GACA|acga
Donor increased54776wt: 0.52 / mu: 0.74wt: CAACGAGATGCCCCC
mu: CAACAAGATGCCCCC		 ACGA|gatg
Donor increased54771wt: 0.26 / mu: 0.94wt: TCAGACAACGAGATG
mu: TCAGACAACAAGATG		 AGAC|aacg
distance from splice site 78
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      191HSADRDWYSDNEMPPEALSQGCKD
mutated  all conserved    191SADRDWYSDNKMPPEALSQGCK
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  191SADRDWYSDNEMPPEALSQGCK
Fcatus  all identical  ENSFCAG00000002960  191SADRDWYSDNEMPPEALSQGCK
Mmusculus  all identical  ENSMUSG00000028766  191SADRDWYSDNEMPPEALSQGCK
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004463  192HSVDRDWLSDSVMPAEAVQDGCK
Drerio  all conserved  ENSDARG00000015546  228DRDWYSDADMPNEALQSGCK
Dmelanogaster  all identical  FBgn0043791  226HLANRNWENDAEVVGD
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 571
cDNA position
(for ins/del: last normal base / first normal base)		 825
gDNA position
(for ins/del: last normal base / first normal base)		 54775
chromosomal position
(for ins/del: last normal base / first normal base)		 21890632
original gDNA sequence snippet GGGACTGGTACTCAGACAACGAGATGCCCCCTGAGGCCTTG
altered gDNA sequence snippet GGGACTGGTACTCAGACAACAAGATGCCCCCTGAGGCCTTG
original cDNA sequence snippet GGGACTGGTACTCAGACAACGAGATGCCCCCTGAGGCCTTG
altered cDNA sequence snippet GGGACTGGTACTCAGACAACAAGATGCCCCCTGAGGCCTTG
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 HATPSAAYAH
SADRDWYSDN KMPPEALSQG 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 1.08 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