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mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • 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 ENST00000539907
Genbank transcript ID NM_001177520
UniProt peptide P05186
alteration type single base exchange
alteration region intron
DNA changes g.51763G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 382
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
2929CONFLICTW -> A (in Ref. 10; AA sequence).might get lost (downstream of altered splice site)
6060METALZinc 2 (Potential).might get lost (downstream of altered splice site)
6060METALMagnesium (Potential).might get lost (downstream of altered splice site)
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 N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 208 / 208
chromosome 1
strand 1
last intron/exon boundary 1286
theoretical NMD boundary in CDS 1028
length of CDS 1344
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
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 N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
mutated AA sequence N/A
speed 0.61 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