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mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM930017)
  • known disease mutation: rs13672 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21902229G>AN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000374829
Genbank transcript ID N/A
UniProt peptide P05186
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.270G>A
g.66372G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918009
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13672 (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 CM930017)

known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930017)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2541
3.6631
(flanking)0.4761
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -21) | splice site change before start ATG (at aa -20) | splice site change before start ATG (at aa -19) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased66369wt: 0.2689 / mu: 0.3238 (marginal change - not scored)wt: CTTTGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGC
mu: CTTTGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGC		 aagg|AGGC
Donor increased66374wt: 0.50 / mu: 0.84wt: GAGGCAGAATTGACC
mu: GAGACAGAATTGACC		 GGCA|gaat
Donor increased66370wt: 0.59 / mu: 0.68wt: CAAGGAGGCAGAATT
mu: CAAGGAGACAGAATT		 AGGA|ggca
Donor increased66365wt: 0.63 / mu: 0.71wt: TGTCCCAAGGAGGCA
mu: TGTCCCAAGGAGACA		 TCCC|aagg
Donor increased66372wt: 0.37 / mu: 0.90wt: AGGAGGCAGAATTGA
mu: AGGAGACAGAATTGA		 GAGG|caga
Donor gained663670.67mu: TCCCAAGGAGACAGA CCAA|ggag
distance from splice site 4
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
117SIGNALmight get lost (downstream of altered splice site)
2929CONFLICTW -> A (in Ref. 10; AA sequence).might get lost (downstream of altered splice site)
6060METALZinc 2 (Potential).might get lost (downstream of altered splice site)
6060METALMagnesium (Potential).might get lost (downstream of altered splice site)
104104CONFLICTN -> K (in Ref. 3; CAA32376).might get lost (downstream of altered splice site)
110110ACT_SITEPhosphoserine intermediate.might get lost (downstream of altered splice site)
140140CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
173173METALMagnesium (Potential).might get lost (downstream of altered splice site)
230230CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 332 / 332
chromosome 1
strand 1
last intron/exon boundary 579
theoretical NMD boundary in CDS 197
length of CDS 513
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 270
gDNA position
(for ins/del: last normal base / first normal base)		 66372
chromosomal position
(for ins/del: last normal base / first normal base)		 21902229
original gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGGCAGAATTGACCACGGGCACC
altered gDNA sequence snippet TGCCTTGGTGTCCCAAGGAGACAGAATTGACCACGGGCACC
original cDNA sequence snippet GCCAGAAACCAGCGGTGGAGGCAGAATTGACCACGGGCACC
altered cDNA sequence snippet GCCAGAAACCAGCGGTGGAGACAGAATTGACCACGGGCACC
wildtype AA sequence MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *
mutated AA sequence N/A
speed 0.61 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