Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999916203667 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920020)
  • known disease mutation: rs13666 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21890681A>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 CDS
DNA changes c.389A>C
cDNA.596A>C
g.54824A>C
AA changes Q130P Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 130
frameshift no
known variant Reference ID: rs121918004
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs13666 (pathogenic for Infantile hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920020)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920020)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2841
4.3771
(flanking)2.1081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased54832wt: 0.51 / mu: 0.82wt: ACATCGCCTACCAGCTCATGCATAACATCAGGGACATTGAC
mu: ACATCGCCTACCCGCTCATGCATAACATCAGGGACATTGAC		 atgc|ATAA
Donor marginally increased54825wt: 0.8481 / mu: 0.8504 (marginal change - not scored)wt: TACCAGCTCATGCAT
mu: TACCCGCTCATGCAT		 CCAG|ctca
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      130ALSQGCKDIAYQLMHNIRDIDVIM
mutated  not conserved    130SQGCKDIAYPLMHNIRDIDVI
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  207ALSQGCKDIAYQLVHNIRDIDVI
Fcatus  all identical  ENSFCAG00000002960  207ALSQGCKDIAYQLMHNVRDIEVI
Mmusculus  all identical  ENSMUSG00000028766  207ALSQGCKDIAYQLMHNIKDIDVI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  208QDGCKDIARQLFENIPDINVI
Drerio  all identical  ENSDARG00000015546  244ALQSGCKDIARQLFENIPDINVI
Dmelanogaster  all identical  FBgn0043791  244NGDPDLCPDAAAQLINSPVGQK
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 1344 / 1344
position (AA) of stopcodon in wt / mu AA sequence 448 / 448
position of stopcodon in wt / mu cDNA 1551 / 1551
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 389
cDNA position
(for ins/del: last normal base / first normal base)		 596
gDNA position
(for ins/del: last normal base / first normal base)		 54824
chromosomal position
(for ins/del: last normal base / first normal base)		 21890681
original gDNA sequence snippet CTGTAAGGACATCGCCTACCAGCTCATGCATAACATCAGGG
altered gDNA sequence snippet CTGTAAGGACATCGCCTACCCGCTCATGCATAACATCAGGG
original cDNA sequence snippet CTGTAAGGACATCGCCTACCAGCTCATGCATAACATCAGGG
altered cDNA sequence snippet CTGTAAGGACATCGCCTACCCGCTCATGCATAACATCAGGG
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 MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYP 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*
speed 1.07 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