ARIH2
ariadne RBR E3 ubiquitin protein ligase 2, the group of RBR E3 ubiquitin ligases
Basic information
Region (hg38): 3:48918821-48986382
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 ARIH2 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 | 0 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in ARIH2
This is a list of pathogenic ClinVar variants found in the ARIH2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-48927757-A-C | not specified | Uncertain significance (Nov 15, 2021) | ||
| 3-48964930-A-G | not specified | Uncertain significance (May 22, 2023) | ||
| 3-48964947-G-T | not specified | Uncertain significance (Aug 05, 2023) | ||
| 3-48967125-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 3-48967254-G-A | not specified | Likely benign (Oct 06, 2021) | ||
| 3-48967266-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 3-48968556-C-G | not specified | Uncertain significance (Nov 29, 2023) | ||
| 3-48968603-A-G | not specified | Uncertain significance (Mar 20, 2024) | ||
| 3-48970646-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
| 3-48973775-G-A | Myoepithelial tumor | Uncertain significance (Nov 01, 2022) | ||
| 3-48981711-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 3-48982973-C-G | not specified | Uncertain significance (Sep 07, 2022) | ||
| 3-48983196-C-T | Autism spectrum disorder | Likely pathogenic (-) | ||
| 3-48983224-C-T | not specified | Uncertain significance (Nov 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARIH2 | protein_coding | protein_coding | ENST00000356401 | 14 | 67562 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00626 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.58 | 118 | 289 | 0.408 | 0.0000161 | 3298 |
| Missense in Polyphen | 21 | 100.13 | 0.20973 | 1222 | ||
| Synonymous | 0.385 | 100 | 105 | 0.952 | 0.00000616 | 833 |
| Loss of Function | 4.89 | 5 | 37.1 | 0.135 | 0.00000200 | 402 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000181 | 0.000181 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase, which catalyzes ubiquitination of target proteins together with ubiquitin- conjugating enzyme E2 UBE2L3 (PubMed:16118314, PubMed:17646546, PubMed:19340006, PubMed:24076655). Acts as an atypical E3 ubiquitin-protein ligase by working together with cullin-5-RING ubiquitin ligase complex (ECS complex, also named CRL5 complex) and initiating ubiquitination of ECS substrates: associates with ECS complex and specifically mediates addition of the first ubiquitin on ECS targets (By similarity). The initial ubiquitin is then elongated (By similarity). E3 ubiquitin-protein ligase activity is activated upon binding to neddylated form of the ECS complex (PubMed:24076655). Mediates 'Lys-6', 'Lys-48'-and 'Lys- 63'-linked polyubiquitination (PubMed:16118314, PubMed:17646546, PubMed:19340006). May play a role in myelopoiesis (PubMed:19340006). {ECO:0000250|UniProtKB:Q9Y4X5, ECO:0000269|PubMed:16118314, ECO:0000269|PubMed:17646546, ECO:0000269|PubMed:19340006, ECO:0000269|PubMed:24076655}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.0818
Intolerance Scores
- loftool
- 0.187
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 32.94
Haploinsufficiency Scores
- pHI
- 0.0609
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.959
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arih2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;ubiquitin-dependent protein catabolic process;multicellular organism development;protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;developmental cell growth;protein K63-linked ubiquitination;protein K48-linked ubiquitination;hematopoietic stem cell proliferation;positive regulation of protein targeting to mitochondrion
- Cellular component
- ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;Cul5-RING ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin conjugating enzyme binding;ubiquitin protein ligase activity