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 CM067338)
- known disease mutation: rs13684 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:21896819C>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | ALPL |
| Ensembl transcript ID | ENST00000374830 |
| Genbank transcript ID | N/A |
| UniProt peptide | P05186 |
| alteration type | single base exchange |
| alteration region | 5'UTR |
| DNA changes | cDNA.24C>T
g.60962C>T |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs121918020
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | - | - | - |
| ExAC | 0 | 2 | 2 |
known disease mutation: rs13684 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|not provided) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM067338)
known disease mutation at this position, please check HGMD for details (HGMD ID CM067338)
known disease mutation at this position, please check HGMD for details (HGMD ID CM067338)
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 3.517 | 1 | | 3.055 | 1 | | (flanking) | 3.033 | 1 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | splice site change before start ATG (at aa -36) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acc marginally increased | 60952 | wt: 0.2756 / mu: 0.3056 (marginal change - not scored) | wt: TCCTCCTAGCACTCCCACTTCATCTGGAACCGCACGGAACT
mu: TCCTCCTAGCACTCCCACTTCATCTGGAACTGCACGGAACT | cttc|ATCT | | Acc increased | 60966 | wt: 0.24 / mu: 0.39 | wt: CCACTTCATCTGGAACCGCACGGAACTCCTGACCCTTGACC
mu: CCACTTCATCTGGAACTGCACGGAACTCCTGACCCTTGACC | gcac|GGAA | | Donor marginally increased | 60965 | wt: 0.9333 / mu: 0.9545 (marginal change - not scored) | wt: ACCGCACGGAACTCC
mu: ACTGCACGGAACTCC | CGCA|cgga | | Donor gained | 60966 | 0.39 | mu: CTGCACGGAACTCCT | GCAC|ggaa |
|
| distance from splice site | 24 |
| Kozak consensus sequence altered? | no |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 17 | SIGNAL | | might get lost (downstream of altered splice site) | | 29 | 29 | CONFLICT | W -> A (in Ref. 10; AA sequence). | might get lost (downstream of altered splice site) | | 60 | 60 | METAL | Zinc 2 (Potential). | might get lost (downstream of altered splice site) | | 60 | 60 | METAL | Magnesium (Potential). | might get lost (downstream of altered splice site) | | 104 | 104 | CONFLICT | N -> K (in Ref. 3; CAA32376). | might get lost (downstream of altered splice site) | | 110 | 110 | ACT_SITE | Phosphoserine intermediate. | might get lost (downstream of altered splice site) | | 140 | 140 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 173 | 173 | METAL | Magnesium (Potential). | might get lost (downstream of altered splice site) | | 230 | 230 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 271 | 271 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 303 | 303 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 332 | 332 | METAL | Magnesium (Potential). | might get lost (downstream of altered splice site) | | 337 | 337 | METAL | Zinc 1 (Potential). | might get lost (downstream of altered splice site) | | 341 | 341 | METAL | Zinc 1 (Potential). | might get lost (downstream of altered splice site) | | 361 | 361 | CONFLICT | Q -> H (in Ref. 1; BAA32129). | might get lost (downstream of altered splice site) | | 378 | 378 | METAL | Zinc 2 (Potential). | might get lost (downstream of altered splice site) | | 379 | 379 | METAL | Zinc 2 (Potential). | might get lost (downstream of altered splice site) | | 430 | 430 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 446 | 446 | CONFLICT | A -> P (in Ref. 1; BAA32129). | might get lost (downstream of altered splice site) | | 454 | 454 | METAL | Zinc 1 (Potential). | might get lost (downstream of altered splice site) | | 502 | 502 | LIPID | GPI-anchor amidated serine (Probable). | might get lost (downstream of altered splice site) | | 503 | 524 | PROPEP | Removed in mature form (Probable). /FTId=PRO_0000024024. | might get lost (downstream of altered splice site) |
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| 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 | 138 / 138 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 385 |
| 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) | 24 |
gDNA position
(for ins/del: last normal base / first normal base) | 60962 |
chromosomal position
(for ins/del: last normal base / first normal base) | 21896819 |
| original gDNA sequence snippet | ACTCCCACTTCATCTGGAACCGCACGGAACTCCTGACCCTT |
| altered gDNA sequence snippet | ACTCCCACTTCATCTGGAACTGCACGGAACTCCTGACCCTT |
| original cDNA sequence snippet | ACTCCCACTTCATCTGGAACCGCACGGAACTCCTGACCCTT |
| altered cDNA sequence snippet | ACTCCCACTTCATCTGGAACTGCACGGAACTCCTGACCCTT |
| 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 | 0.67 s |
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