Prediction |
polymorphism |
Model: without_aae, prob: 4.52057899848994e-12 (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) | chr3:52861211A>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | ITIH4 |
| Ensembl transcript ID | ENST00000434759 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q14624 |
| alteration type | single base exchange |
| alteration region | 5'UTR |
| DNA changes | cDNA.139T>A
g.4285T>A |
| AA changes | N/A |
position(s) of altered AA
if AA alteration in CDS | N/A |
| frameshift | N/A |
| known variant | Reference ID: rs13072536
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | 166 | 896 | 1062 |
| ExAC | 4308 | 21445 | 25753 |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 0.966 | 0.991 | | 0.606 | 0.979 | | (flanking) | -0.115 | 0.967 |
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
| splice sites | alteration within used splice site, likely to disturb normal splicing
splice site change before start ATG (at aa -3) | splice site change before start ATG (at aa -1) | | effect | gDNA position | score | detection sequence | exon-intron border | | Acceptor lost | 4282.5 | sequence motif lost | - | wt: ccca|GGAT
mu: ccca.GGAA | | Acc marginally increased | 4281 | wt: 0.8712 / mu: 0.8733 (marginal change - not scored) | wt: ACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACC
mu: ACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACC | ccca|GGAT | | Acc marginally increased | 4275 | wt: 0.2184 / mu: 0.2264 (marginal change - not scored) | wt: TCAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGC
mu: TCAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGC | tctg|CCCC | | Acc marginally increased | 4282 | wt: 0.9638 / mu: 0.9676 (marginal change - not scored) | wt: CTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCT
mu: CTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCT | ccag|GATC | | Acc marginally increased | 4276 | wt: 0.5850 / mu: 0.5963 (marginal change - not scored) | wt: CAACAACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCA
mu: CAACAACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCA | ctgc|CCCC | | Acc marginally increased | 4280 | wt: 0.6087 / mu: 0.6576 (marginal change - not scored) | wt: AACTCCCACCCTTCTGCCCCCAGGATCATCGATGGCATGAC
mu: AACTCCCACCCTTCTGCCCCCAGGAACATCGATGGCATGAC | cccc|AGGA | | Donor increased | 4281 | wt: 0.26 / mu: 0.92 | wt: CCCCCAGGATCATCG
mu: CCCCCAGGAACATCG | CCCA|ggat | | Donor increased | 4287 | wt: 0.37 / mu: 0.47 | wt: GGATCATCGATGGCA
mu: GGAACATCGATGGCA | ATCA|tcga |
|
| distance from splice site | 3 |
| Kozak consensus sequence altered? | no |
conservation
protein level for non-synonymous changes | N/A |
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 28 | SIGNAL | | might get lost (downstream of altered splice site) | | 29 | 148 | DOMAIN | VIT. | might get lost (downstream of altered splice site) | | 81 | 81 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 85 | 85 | CONFLICT | I -> K (in Ref. 3; AAD05198). | might get lost (downstream of altered splice site) | | 114 | 114 | CONFLICT | S -> N (in Ref. 2; BAA07602). | might get lost (downstream of altered splice site) | | 207 | 207 | CONFLICT | N -> F (in Ref. 5; AA sequence). | might get lost (downstream of altered splice site) | | 207 | 207 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 221 | 221 | CONFLICT | Q -> E (in Ref. 5; AA sequence). | might get lost (downstream of altered splice site) | | 272 | 432 | DOMAIN | VWFA. | might get lost (downstream of altered splice site) | | 307 | 307 | CONFLICT | R -> V (in Ref. 5; AA sequence). | might get lost (downstream of altered splice site) | | 322 | 322 | CONFLICT | W -> Y (in Ref. 5; AA sequence). | might get lost (downstream of altered splice site) | | 517 | 517 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 577 | 577 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 662 | 688 | PROPEP | Potentially active peptide. /FTId=PRO_0000016542. | might get lost (downstream of altered splice site) | | 696 | 696 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | | 701 | 701 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | | 702 | 702 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | | 719 | 725 | REGION | O-glycosylated at three sites. | might get lost (downstream of altered splice site) | | 720 | 720 | CARBOHYD | O-linked (GalNAc...). | might get lost (downstream of altered splice site) | | 747 | 747 | DISULFID | Probable. | might get lost (downstream of altered splice site) | | 816 | 817 | CONFLICT | ET -> QR (in Ref. 5; AA sequence). | might get lost (downstream of altered splice site) | | 925 | 925 | DISULFID | Probable. | 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 | 150 / 150 |
| chromosome | 3 |
| strand | -1 |
| last intron/exon boundary | 1984 |
| theoretical NMD boundary in CDS | 1784 |
| length of CDS | 1683 |
| coding sequence (CDS) position | N/A |
cDNA position
(for ins/del: last normal base / first normal base) | 139 |
gDNA position
(for ins/del: last normal base / first normal base) | 4285 |
chromosomal position
(for ins/del: last normal base / first normal base) | 52861211 |
| original gDNA sequence snippet | CCACCCTTCTGCCCCCAGGATCATCGATGGCATGACCTACC |
| altered gDNA sequence snippet | CCACCCTTCTGCCCCCAGGAACATCGATGGCATGACCTACC |
| original cDNA sequence snippet | ACTACTACTGCCGAAAAGGATCATCGATGGCATGACCTACC |
| altered cDNA sequence snippet | ACTACTACTGCCGAAAAGGAACATCGATGGCATGACCTACC |
| wildtype AA sequence | MTYPGIIKEK AEAQAQYSAA VAKGKSAGLV KATGRNMEQF QVSVSVAPNA KITFELVYEE
LLKRRLGVYE LLLKVRPQQL VKHLQMDIHI FEPQGISFLE TESTFMTNQL VDALTTWQNK
TKAHIRFKPT LSQQQKSPEQ QETVLDGNLI IRYDVDRAIS GGSIQIENGY FVHYFAPEGL
TTMPKNVVFV IDKSGSMSGR KIQQTREALI KILDDLSPRD QFNLIVFSTE ATQWRPSLVP
ASAENVNKAR SFAAGIQALG GTNINDAMLM AVQLLDSSNQ EERLPEGSVS LIILLTDGDP
TVGETNPRSI QNNVREAVSG RYSLFCLGFG FDVSYAFLEK LALDNGGLAR RIHEDSDSAL
QLQDFYQEVA NPLLTAVTFE YPSNAVEEVT QNNFRLLFKG SEMVVAGKLQ DRGPDVLTAT
VSGKLPTQNI TFQTESSVAE QEAEFQSPKY IFHNFMERLW AYLTIQQLLE QTVSASDADQ
QALRNQALNL SLAYSFVTPL TSMVVTKPDD QEQSQVAEKP MEGESRNRNV HSGSTFFKYY
LQGAKIPKPG DKVGGGGRGD * |
| mutated AA sequence | N/A |
| speed | 0.40 s |
|
|
