Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999994550109954 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012062)
  • known disease mutation: rs13679 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21903075A>GN/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.1019A>G
cDNA.1226A>G
g.67218A>G
AA changes N340S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 340
frameshift no
known variant Reference ID: rs121918014
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs13679 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Hypophosphatasia, perinatal lethal|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1151
4.1151
(flanking)0.1820.998
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 increased67211wt: 0.7942 / mu: 0.8654 (marginal change - not scored)wt: AGCCCTTCACTGCCATCCTGTATGGCAATGGGCCTGGCTAC
mu: AGCCCTTCACTGCCATCCTGTATGGCAGTGGGCCTGGCTAC		 ctgt|ATGG
Acc marginally increased67209wt: 0.8277 / mu: 0.8375 (marginal change - not scored)wt: GAAGCCCTTCACTGCCATCCTGTATGGCAATGGGCCTGGCT
mu: GAAGCCCTTCACTGCCATCCTGTATGGCAGTGGGCCTGGCT		 tcct|GTAT
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      340DKKPFTAILYGNGPGYKVVGGERE
mutated  all conserved    340DKKPFTAILYGSGPGYKVVGGER
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  417DKKPFTAILYGNGPGYKVVGGER
Fcatus  all identical  ENSFCAG00000002960  417DKKPFTSILYGNGPGYKVVGGER
Mmusculus  all identical  ENSMUSG00000028766  417DKKPFTAILYGNGPGYKVVDGER
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  417DQKPFTAILYGNGPGYKLVNGGR
Drerio  all identical  ENSDARG00000015546  453DQKPFTAILYGNGPGFKLVNGAR
Dmelanogaster  all identical  FBgn0043791  451DDLPYATLSYANGPGYDSNYLREGGAVRR
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 1019
cDNA position
(for ins/del: last normal base / first normal base)		 1226
gDNA position
(for ins/del: last normal base / first normal base)		 67218
chromosomal position
(for ins/del: last normal base / first normal base)		 21903075
original gDNA sequence snippet CACTGCCATCCTGTATGGCAATGGGCCTGGCTACAAGGTGG
altered gDNA sequence snippet CACTGCCATCCTGTATGGCAGTGGGCCTGGCTACAAGGTGG
original cDNA sequence snippet CACTGCCATCCTGTATGGCAATGGGCCTGGCTACAAGGTGG
altered cDNA sequence snippet CACTGCCATCCTGTATGGCAGTGGGCCTGGCTACAAGGTGG
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 GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGS GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
speed 1.09 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