Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999992823180901 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920021)
  • known disease mutation: rs13664 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21900176A>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.650A>C
cDNA.857A>C
g.64319A>C
AA changes D217A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 217
frameshift no
known variant Reference ID: rs121918002
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13664 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.6791
3.8781
(flanking)0.9651
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased64314wt: 0.2939 / mu: 0.3341 (marginal change - not scored)wt: TCCTCAGGTCTCTTCGAGCCAGGGGACATGCAGTACGAGCT
mu: TCCTCAGGTCTCTTCGAGCCAGGGGCCATGCAGTACGAGCT		 gcca|GGGG
Donor marginally increased64310wt: 0.9845 / mu: 0.9945 (marginal change - not scored)wt: CTTCGAGCCAGGGGA
mu: CTTCGAGCCAGGGGC		 TCGA|gcca
Donor marginally increased64317wt: 0.9286 / mu: 0.9491 (marginal change - not scored)wt: CCAGGGGACATGCAG
mu: CCAGGGGCCATGCAG		 AGGG|gaca
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      217VDYLLGLFEPGDMQYELNRNNVTD
mutated  not conserved    217VDYLLGLFEPGAMQYELNRNNVT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  294VDYLLGLFEPGDMEYELNRNNVT
Fcatus  all identical  ENSFCAG00000002960  294VDYLLGLFEPGDMQYELNRNSTT
Mmusculus  all identical  ENSMUSG00000028766  294VDYLLGLFEPGDMQYELNRNNLT
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  295VDYLLGLFEPEDMTYDLERNPET
Drerio  all identical  ENSDARG00000015546  330VDYLLGLFEPADLNYELERNTEN
Dmelanogaster  not conserved  FBgn0043791  327-SRVLGLFAPYHMAYHLDASPAE
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
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 650
cDNA position
(for ins/del: last normal base / first normal base)		 857
gDNA position
(for ins/del: last normal base / first normal base)		 64319
chromosomal position
(for ins/del: last normal base / first normal base)		 21900176
original gDNA sequence snippet AGGTCTCTTCGAGCCAGGGGACATGCAGTACGAGCTGAACA
altered gDNA sequence snippet AGGTCTCTTCGAGCCAGGGGCCATGCAGTACGAGCTGAACA
original cDNA sequence snippet GGGTCTCTTCGAGCCAGGGGACATGCAGTACGAGCTGAACA
altered cDNA sequence snippet GGGTCTCTTCGAGCCAGGGGCCATGCAGTACGAGCTGAACA
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
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGAMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
speed 1.04 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