Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999996488940009 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920016)
  • known disease mutation: rs13667 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21887155C>TN/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.98C>T
cDNA.98C>T
g.51298C>T
AA changes A33V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 33
frameshift no
known variant Reference ID: rs121918005
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8631
3.8630.998
(flanking)-1.5660.187
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 increased51291wt: 0.9088 / mu: 0.9923 (marginal change - not scored)wt: GGCGAGACCAAGCGC
mu: GGCGAGACCAAGTGC		 CGAG|acca
Donor marginally increased51302wt: 0.8397 / mu: 0.8869 (marginal change - not scored)wt: GCGCAAGAGACACTG
mu: GTGCAAGAGACACTG		 GCAA|gaga
Donor marginally increased51296wt: 0.3412 / mu: 0.3481 (marginal change - not scored)wt: GACCAAGCGCAAGAG
mu: GACCAAGTGCAAGAG		 CCAA|gcgc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      33KEKDPKYWRDQAQETLKYALELQK
mutated  not conserved    33KEKDPKYWRDQVQETLKYALELQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  33KEKDPKYWRDQAQETLKYALELQ
Fcatus  all identical  ENSFCAG00000002960  33KEKDPKYWRDQAQQTLKNALRLQ
Mmusculus  all identical  ENSMUSG00000028766  33KERDPSYWRQQAQETLKNALKLQ
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  34QEKDPKFWNTWAQQTLKNALSLQ
Drerio  all identical  ENSDARG00000015546  65QEKRPDYWRDFAQRSLKDALKLQ
Dmelanogaster  all identical  FBgn0043791  73EERYAEYWQGLAAQTLDQQLESKL
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 98
cDNA position
(for ins/del: last normal base / first normal base)		 98
gDNA position
(for ins/del: last normal base / first normal base)		 51298
chromosomal position
(for ins/del: last normal base / first normal base)		 21887155
original gDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered gDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
original cDNA sequence snippet CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG
altered cDNA sequence snippet CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG
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 DQVQETLKYA 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*
speed 1.22 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