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 ENST00000425315
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.1250A>G
cDNA.1250A>G
g.67218A>G
AA changes N417S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 417
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      417DKKPFTAILYGNGPGYKVVGGERE
mutated  all conserved    417DKKPFTAILYGSGPG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  417DKKPFTAILYGNGPG
Fcatus  all identical  ENSFCAG00000002960  417DKKPFTSILYGNGPG
Mmusculus  all identical  ENSMUSG00000028766  417DKKPFTAILYGNGPG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  417DQKPFTAILYGNGPGYKLVNGGR
Drerio  all identical  ENSDARG00000015546  453DQKPFTAILYGNGPGFK
Dmelanogaster  all identical  FBgn0043791  451DDLPYATLSYANGPGYDSNYLREGG
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 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1575 / 1575
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 1 / 1
chromosome 1
strand 1
last intron/exon boundary 1310
theoretical NMD boundary in CDS 1259
length of CDS 1575
coding sequence (CDS) position 1250
cDNA position
(for ins/del: last normal base / first normal base)		 1250
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 MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
mutated AA sequence MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGSGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*
speed 1.10 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