Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999961250144 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM077891)
  • known disease mutation at this position (HGMD CM993527)
  • known disease mutation: rs13677 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889651G>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.346G>A
cDNA.596G>A
g.53794G>A
AA changes A116T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 116
frameshift no
known variant Reference ID: rs121918013
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13677 (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 CM993527)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993527)
known disease mutation at this position, please check HGMD for details (HGMD ID CM077891)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993527)
known disease mutation at this position, please check HGMD for details (HGMD ID CM077891)
known disease mutation at this position, please check HGMD for details (HGMD ID CM077891)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993527)
known disease mutation at this position, please check HGMD for details (HGMD ID CM077891)
known disease mutation at this position, please check HGMD for details (HGMD ID CM077891)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993527)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9620.572
5.3071
(flanking)5.3071
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased53805wt: 0.60 / mu: 0.66wt: ACCGCCACCGCCTACCTGTGTGGGGTGAAGGCCAATGAGGG
mu: ACCGCCACCACCTACCTGTGTGGGGTGAAGGCCAATGAGGG		 gtgt|GGGG
Donor marginally increased53798wt: 0.4614 / mu: 0.4617 (marginal change - not scored)wt: CGCCTACCTGTGTGG
mu: CACCTACCTGTGTGG		 CCTA|cctg
Donor increased53787wt: 0.46 / mu: 0.59wt: GGCACCGCCACCGCC
mu: GGCACCGCCACCACC		 CACC|gcca
distance from splice site 49
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      116AQVPDSAGTATAYLCGVKANEGTV
mutated  not conserved    116AQVPDSAGTATTYLCG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  116AQVPDSAGTATAYLCG
Fcatus  all identical  ENSFCAG00000002960  116AQVPDSAGTATAYLCG
Mmusculus  all identical  ENSMUSG00000028766  116AQVPDSAGTATAYLCG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  117AQVADSAGTATAFLCGVKANEGT
Drerio  all identical  ENSDARG00000015546  153AQVPDSAGTATAFLCGVK
Dmelanogaster  all identical  FBgn0043791  155MQVADSACTATAYLGGVKANYGT
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
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 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 346
cDNA position
(for ins/del: last normal base / first normal base)		 596
gDNA position
(for ins/del: last normal base / first normal base)		 53794
chromosomal position
(for ins/del: last normal base / first normal base)		 21889651
original gDNA sequence snippet ACAGTGCCGGCACCGCCACCGCCTACCTGTGTGGGGTGAAG
altered gDNA sequence snippet ACAGTGCCGGCACCGCCACCACCTACCTGTGTGGGGTGAAG
original cDNA sequence snippet ACAGTGCCGGCACCGCCACCGCCTACCTGTGTGGGGTGAAG
altered cDNA sequence snippet ACAGTGCCGGCACCGCCACCACCTACCTGTGTGGGGTGAAG
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 AGTATTYLCG
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 1.28 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