Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999969913587 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM031931)
  • known disease mutation: rs13680 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21889628C>TN/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.92C>T
cDNA.299C>T
g.53771C>T
AA changes P31L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 31
frameshift no
known variant Reference ID: rs121918015
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13680 (pathogenic for Odontohypophosphatasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031931)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031931)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031931)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.7151
5.3981
(flanking)-2.9510.032
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 increased53776wt: 0.6998 / mu: 0.7431 (marginal change - not scored)wt: CTGACAGTGCCGGCA
mu: TTGACAGTGCCGGCA		 GACA|gtgc
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      31WEMTYNTNAQVPDSAGTATAYLCG
mutated  not conserved    31WEMTYNTNAQVLDSAGTATAYLC
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  108TYNTNAQVPDSAGTATAYLC
Fcatus  all identical  ENSFCAG00000002960  108TYNTNAQVPDSAGTATAYLC
Mmusculus  all identical  ENSMUSG00000028766  108TYNTNAQVPDSAGTATAYLC
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004463  106LAKTYNTNAQVADSAGTATAFLC
Drerio  all identical  ENSDARG00000015546  145TYNTNAQVPDSAGTATAFLC
Dmelanogaster  not conserved  FBgn0043791  143TYCANMQVADSACTATAYLG
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 92
cDNA position
(for ins/del: last normal base / first normal base)		 299
gDNA position
(for ins/del: last normal base / first normal base)		 53771
chromosomal position
(for ins/del: last normal base / first normal base)		 21889628
original gDNA sequence snippet CAACACCAATGCCCAGGTCCCTGACAGTGCCGGCACCGCCA
altered gDNA sequence snippet CAACACCAATGCCCAGGTCCTTGACAGTGCCGGCACCGCCA
original cDNA sequence snippet CAACACCAATGCCCAGGTCCCTGACAGTGCCGGCACCGCCA
altered cDNA sequence snippet CAACACCAATGCCCAGGTCCTTGACAGTGCCGGCACCGCCA
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 LDSAGTATAY 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*
speed 0.48 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