Prediction |
polymorphism |
Model: without_aae, prob: 1.20473560988449e-09 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM176738)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr10:91007360T>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | LIPA |
| Ensembl transcript ID | ENST00000371837 |
| Genbank transcript ID | N/A |
| UniProt peptide | P38571 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.167023A>C |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs1051338
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 246 | 941 | 1187 |
| ExAC | 6489 | 19789 | 26278 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM176738)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.861 | 0.901 | | 1.195 | 0.98 | | (flanking) | 0.883 | 0.995 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | | effect | gDNA position | score | wt detection sequence | exon-intron border | | Acc increased | 167029 | wt: 0.44 / mu: 0.82 | wt: GTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAGGG
mu: GTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGG | ctgc|ATTC | | Acc increased | 167027 | wt: 0.76 / mu: 0.88 | wt: CTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAG
mu: CTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAG | ccct|GCAT | | Acc increased | 167031 | wt: 0.65 / mu: 0.91 | wt: TTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAGGGAA
mu: TTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAA | gcat|TCTG | | Acc marginally increased | 167013 | wt: 0.2716 / mu: 0.2933 (marginal change - not scored) | wt: TTGGGGTTGGTGGTCTGTTTGGTTCTCTGGACCCTGCATTC
mu: TTGGGGTTGGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTC | tttg|GTTC | | Acc marginally increased | 167014 | wt: 0.2238 / mu: 0.2331 (marginal change - not scored) | wt: TGGGGTTGGTGGTCTGTTTGGTTCTCTGGACCCTGCATTCT
mu: TGGGGTTGGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTCT | ttgg|TTCT | | Acc marginally increased | 167021 | wt: 0.9597 / mu: 0.9663 (marginal change - not scored) | wt: GGTGGTCTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGT
mu: GGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGT | tctg|GACC | | Acc gained | 167033 | 0.43 | mu: GGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAAAC | attc|TGAG | | Acc gained | 167025 | 0.61 | mu: GTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGG | gccc|CTGC | | Acc gained | 167034 | 0.42 | mu: GTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAAACT | ttct|GAGG |
|
| distance from splice site | 19205 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 21 | SIGNAL | Potential. | might get lost (downstream of altered splice site) | | 36 | 36 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 72 | 72 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 101 | 101 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 161 | 161 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 174 | 174 | ACT_SITE | Charge relay system (By similarity). | might get lost (downstream of altered splice site) | | 273 | 273 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 321 | 321 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 374 | 374 | ACT_SITE | Charge relay system (By similarity). | might get lost (downstream of altered splice site) | | 397 | 397 | CONFLICT | K -> R (in Ref. 5; BAD96480). | 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 | 223 / 223 |
| chromosome | 10 |
| strand | -1 |
| last intron/exon boundary | 1021 |
| theoretical NMD boundary in CDS | 748 |
| length of CDS | 1032 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | N/A |
gDNA position
(for ins/del: last normal base / first normal base) | 167023 |
chromosomal position
(for ins/del: last normal base / first normal base) | 91007360 |
| original gDNA sequence snippet | TGGTCTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCT |
| altered gDNA sequence snippet | TGGTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCT |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MACLEFVPFD VQMCLEFLPS GPKPVVFLQH GLLADSSNWV TNLANSSLGF ILADAGFDVW
MGNSRGNTWS RKHKTLSVSQ DEFWAFSYDE MAKYDLPASI NFILNKTGQE QVYYVGHSQG
TTIGFIAFSQ IPELAKRIKM FFALGPVASV AFCTSPMAKL GRLPDHLIKD LFGDKEFLPQ
SAFLKWLGTH VCTHVILKEL CGNLCFLLCG FNERNLNMSR VDVYTTHSPA GTSVQNMLHW
SQAVKFQKFQ AFDWGSSAKN YFHYNQSYPP TYNVKDMLVP TAVWSGGHDW LADVYDVNIL
LTQITNLVFH ESIPEWEHLD FIWGLDAPWR LYNKIINLMR KYQ* |
| mutated AA sequence | N/A |
| speed | 0.77 s |
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