RCHY1
Basic information
Region (hg38): 4:75479032-75514764
Previous symbols: [ "ZNF363" ]
Links
Phenotypes
GenCC
Source:
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 RCHY1 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 1 |
Variants in RCHY1
This is a list of pathogenic ClinVar variants found in the RCHY1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-75482563-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 4-75482564-G-A | not specified | Likely benign (Mar 29, 2024) | ||
| 4-75482611-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 4-75482647-T-C | not specified | Uncertain significance (Apr 25, 2022) | ||
| 4-75509215-T-C | not specified | Uncertain significance (Nov 08, 2022) | ||
| 4-75509247-T-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 4-75514219-T-C | not specified | Uncertain significance (Jun 18, 2024) | ||
| 4-75514253-C-A | not specified | Uncertain significance (Dec 13, 2023) | ||
| 4-75514254-G-C | not specified | Likely benign (Jan 03, 2024) | ||
| 4-75514275-C-T | Benign (May 15, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RCHY1 | protein_coding | protein_coding | ENST00000324439 | 9 | 35728 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0662 | 0.931 | 125712 | 0 | 36 | 125748 | 0.000143 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.20 | 101 | 141 | 0.715 | 0.00000701 | 1737 |
| Missense in Polyphen | 32 | 66.802 | 0.47903 | 798 | ||
| Synonymous | 1.04 | 37 | 46.0 | 0.805 | 0.00000218 | 427 |
| Loss of Function | 2.63 | 5 | 16.5 | 0.302 | 7.81e-7 | 221 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000810 | 0.000749 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000191 | 0.000185 |
| European (Non-Finnish) | 0.000110 | 0.000105 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000670 | 0.0000653 |
| Other | 0.000208 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates E3-dependent ubiquitination and proteasomal degradation of target proteins, including p53/TP53, P73, HDAC1 and CDKN1B. Preferentially acts on tetrameric p53/TP53. Monoubiquitinates the translesion DNA polymerase POLH. Contributes to the regulation of the cell cycle progression. Increases AR transcription factor activity. {ECO:0000269|PubMed:16914734, ECO:0000269|PubMed:17721809, ECO:0000269|PubMed:18006823, ECO:0000269|PubMed:19043414, ECO:0000269|PubMed:19483087, ECO:0000269|PubMed:21791603, ECO:0000269|PubMed:21994467}.;
- Pathway
- p53 signaling pathway - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);Measles - Homo sapiens (human);DNA Repair;Immune System;Adaptive Immune System;p73 transcription factor network;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;AndrogenReceptor;Direct p53 effectors;Translesion Synthesis by POLH;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.489
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- 0.349
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.680
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.905
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rchy1
- Phenotype
- cellular phenotype;
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein ubiquitination;positive regulation of protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;error-free translesion synthesis
- Cellular component
- ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;cytosol;nuclear speck
- Molecular function
- p53 binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;protein homodimerization activity