Prediction |
polymorphism |
Model: without_aae, prob: 0.999999730797239 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- homozygous in TGP or ExAC
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr3:50334231T>AN/A
show variant in all transcripts IGV
|
| HGNC symbol | HYAL3 |
| Ensembl transcript ID | ENST00000513170 |
| Genbank transcript ID | NM_001200032 |
| UniProt peptide | O43820 |
| alteration type | single base exchange |
| alteration region | intron |
| DNA changes | g.2669A>T |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs2269432
| database | homozygous (A/A) | heterozygous | allele carriers |
| 1000G | 256 | 578 | 834 |
| ExAC | 2950 | 6792 | 9742 |
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.403 | 0 | | -0.154 | 0.001 | | (flanking) | 0.952 | 0.028 |
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 marginally increased | 2661 | wt: 0.9392 / mu: 0.9465 (marginal change - not scored) | wt: CCCCACAGCCCCCTCTCCCCGGCCACCCAGGAAGGCCCCAA
mu: CCCCACAGCCCCCTCTCCCCGGCCACCCTGGAAGGCCCCAA | cccg|GCCA | | Acc marginally increased | 2660 | wt: 0.8908 / mu: 0.9041 (marginal change - not scored) | wt: TCCCCACAGCCCCCTCTCCCCGGCCACCCAGGAAGGCCCCA
mu: TCCCCACAGCCCCCTCTCCCCGGCCACCCTGGAAGGCCCCA | cccc|GGCC | | Acc marginally increased | 2662 | wt: 0.6046 / mu: 0.6610 (marginal change - not scored) | wt: CCCACAGCCCCCTCTCCCCGGCCACCCAGGAAGGCCCCAAA
mu: CCCACAGCCCCCTCTCCCCGGCCACCCTGGAAGGCCCCAAA | ccgg|CCAC | | Acc gained | 2671 | 0.69 | mu: CCCTCTCCCCGGCCACCCTGGAAGGCCCCAAACCTGACTGC | ctgg|AAGG |
|
| distance from splice site | 1947 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 20 | SIGNAL | Potential. | might get lost (downstream of altered splice site) | | 42 | 42 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 54 | 54 | CONFLICT | A -> S (in Ref. 5; AAH05896). | might get lost (downstream of altered splice site) | | 69 | 69 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 129 | 129 | ACT_SITE | Proton donor (By similarity). | might get lost (downstream of altered splice site) | | 205 | 205 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 215 | 215 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 220 | 220 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 331 | 331 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 352 | 407 | DOMAIN | EGF-like. | might get lost (downstream of altered splice site) | | 356 | 356 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 361 | 361 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 367 | 367 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 395 | 395 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 397 | 397 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 406 | 406 | DISULFID | By similarity. | 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 | 19 / 19 |
| chromosome | 3 |
| strand | -1 |
| last intron/exon boundary | 166 |
| theoretical NMD boundary in CDS | 97 |
| length of CDS | 417 |
| 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) | 2669 |
chromosomal position
(for ins/del: last normal base / first normal base) | 50334231 |
| original gDNA sequence snippet | CCCCCTCTCCCCGGCCACCCAGGAAGGCCCCAAACCTGACT |
| altered gDNA sequence snippet | CCCCCTCTCCCCGGCCACCCTGGAAGGCCCCAAACCTGACT |
| original cDNA sequence snippet | N/A |
| altered cDNA sequence snippet | N/A |
| wildtype AA sequence | MLPPAHHQAF VRHRLEEAFR VALVGHRHPL PVLAYVRLTH RRSGRFLSQE ECWHLHDYLV
DTLGPYVINV TRAAMACSHQ RCHGHGRCAR RDPGQMEAFL HLWPDGSLGD WKSFSCHCYW
GWAGPTCQEP RPGPKEAV* |
| mutated AA sequence | N/A |
| speed | 0.53 s |
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