PEDS1-UBE2V1
PEDS1-UBE2V1 readthrough
Basic information
Region (hg38): 20:50081123-50153637
Previous symbols: [ "TMEM189-UBE2V1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEDS1-UBE2V1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 3 | 0 | 1 |
Variants in PEDS1-UBE2V1
This is a list of pathogenic ClinVar variants found in the PEDS1-UBE2V1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-50082792-G-A | Benign (Apr 13, 2018) | |||
| 20-50125110-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
| 20-50125137-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
| 20-50153533-AG-A | See cases | Uncertain significance (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PEDS1-UBE2V1 | protein_coding | protein_coding | ENST00000341698 | 8 | 72514 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00839 | 0.989 | 125665 | 0 | 8 | 125673 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.43 | 112 | 211 | 0.530 | 0.0000124 | 2374 |
| Missense in Polyphen | 27 | 66.263 | 0.40747 | 630 | ||
| Synonymous | -1.18 | 95 | 81.4 | 1.17 | 0.00000490 | 713 |
| Loss of Function | 2.65 | 7 | 19.7 | 0.356 | 0.00000110 | 203 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000887 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.000166 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Has no ubiquitin ligase activity on its own. The UBE2V1- UBE2N heterodimer catalyzes the synthesis of non-canonical poly- ubiquitin chains that are linked through Lys-63. This type of poly-ubiquitination activates IKK and does not seem to involve protein degradation by the proteasome. Plays a role in the activation of NF-kappa-B mediated by IL1B, TNF, TRAF6 and TRAF2. Mediates transcriptional activation of target genes. Plays a role in the control of progress through the cell cycle and differentiation. Plays a role in the error-free DNA repair pathway and contributes to the survival of cells after DNA damage. Promotes TRIM5 capsid-specific restriction activity and the UBE2V1-UBE2N heterodimer acts in concert with TRIM5 to generate 'Lys-63'-linked polyubiquitin chains which activate the MAP3K7/TAK1 complex which in turn results in the induction and expression of NF-kappa-B and MAPK-responsive inflammatory genes. {ECO:0000269|PubMed:11057907, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:9305758, ECO:0000269|PubMed:9418904, ECO:0000269|PubMed:9580084, ECO:0000269|PubMed:9705497}.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;TLR NFkB;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signaling by Interleukins;TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;B cell receptor signaling;Toll-Like Receptors Cascades;Downstream TCR signaling;TCR signaling;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;protein ubiquitylation;Interleukin-1 signaling;IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;IL-1 NFkB;Class I MHC mediated antigen processing & presentation;IL-1 p38;IL-1 JNK;IL1;TLR p38;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1;activated TAK1 mediates p38 MAPK activation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TLR JNK;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;IRAK1 recruits IKK complex;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;IL1-mediated signaling events;Interleukin-1 family signaling;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.508
- ghis
- 0.399
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0718
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- postreplication repair;protein K63-linked ubiquitination
- Cellular component
- nucleus;nucleoplasm;integral component of membrane
- Molecular function
- ubiquitin conjugating enzyme activity