RNF2
ring finger protein 2, the group of Ring finger proteins
Basic information
Region (hg38): 1:185045525-185102603
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Lou-Schoch-Yamamoto syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 33864376 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (4 variants)
- LUO-SCHOCH-YAMAMOTO SYNDROME (2 variants)
- RNF2-associated neurodevelopmental condition (1 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF2 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 1 | 6 | 7 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 0 | 6 | 0 | 0 |
Variants in RNF2
This is a list of pathogenic ClinVar variants found in the RNF2 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-185087566-G-A | Inborn genetic diseases | Uncertain significance (Aug 02, 2021) | ||
| 1-185087566-G-T | Inborn genetic diseases | Uncertain significance (Mar 29, 2023) | ||
| 1-185091700-G-A | RNF2-associated neurodevelopmental condition • Luo-Schoch-Yamamoto syndrome | Uncertain significance (May 17, 2018) | ||
| 1-185091709-C-T | Inborn genetic diseases | Uncertain significance (Mar 22, 2022) | ||
| 1-185091737-T-G | Luo-Schoch-Yamamoto syndrome | Pathogenic (Aug 19, 2021) | ||
| 1-185093207-A-G | Inborn genetic diseases | Uncertain significance (Jun 13, 2023) | ||
| 1-185098071-G-A | Luo-Schoch-Yamamoto syndrome | Uncertain significance (Sep 01, 2023) | ||
| 1-185098250-G-T | Inborn genetic diseases | Uncertain significance (Oct 12, 2021) | ||
| 1-185098265-A-G | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
| 1-185098265-A-AC | Luo-Schoch-Yamamoto syndrome | Uncertain significance (Feb 20, 2023) | ||
| 1-185098341-C-T | Uncertain significance (Nov 01, 2021) | |||
| 1-185099874-G-A | Inborn genetic diseases | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RNF2 | protein_coding | protein_coding | ENST00000367510 | 6 | 57245 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00257 | 125741 | 0 | 4 | 125745 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 87 | 183 | 0.475 | 0.00000907 | 2238 |
| Missense in Polyphen | 15 | 57.534 | 0.26072 | 751 | ||
| Synonymous | 0.401 | 57 | 61.0 | 0.935 | 0.00000293 | 603 |
| Loss of Function | 3.88 | 0 | 17.5 | 0.00 | 0.00000105 | 199 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A (H2AK119Ub), thereby playing a central role in histone code and gene regulation (PubMed:15386022, PubMed:16359901, PubMed:25519132, PubMed:21772249, PubMed:25355358, PubMed:26151332). H2AK119Ub gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation (By similarity). Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development (PubMed:16359901, PubMed:26151332). PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility (PubMed:26151332). E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4 (PubMed:21772249). Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity (Probable). Association with the chromosomal DNA is cell-cycle dependent. In resting B- and T-lymphocytes, interaction with AURKB leads to block its activity, thereby maintaining transcription in resting lymphocytes (By similarity). {ECO:0000250|UniProtKB:Q9CQJ4, ECO:0000269|PubMed:11513855, ECO:0000269|PubMed:15386022, ECO:0000269|PubMed:16359901, ECO:0000269|PubMed:16714294, ECO:0000269|PubMed:20696397, ECO:0000269|PubMed:21772249, ECO:0000269|PubMed:25355358, ECO:0000269|PubMed:25519132, ECO:0000269|PubMed:26151332, ECO:0000305}.;
- Pathway
- Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oxidative Stress Induced Senescence;SUMOylation of DNA damage response and repair proteins;Cellular Senescence;SUMOylation of chromatin organization proteins;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.450
Intolerance Scores
- loftool
- 0.223
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.634
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf2
- Phenotype
- immune system phenotype; skeleton phenotype; 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); 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); hematopoietic system phenotype; neoplasm; embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- rnf2
- Affected structure
- xanthophore
- Phenotype tag
- abnormal
- Phenotype quality
- decreased branchiness
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;mitotic cell cycle;gastrulation with mouth forming second;germ cell development;anterior/posterior axis specification;histone H2A monoubiquitination;histone H2A-K119 monoubiquitination;negative regulation of DNA-binding transcription factor activity;negative regulation of G0 to G1 transition
- Cellular component
- ubiquitin ligase complex;euchromatin;sex chromatin;nucleus;nucleoplasm;nuclear body;PcG protein complex;PRC1 complex;MLL1 complex
- Molecular function
- chromatin binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin protein ligase activity;RING-like zinc finger domain binding