RAD23A
Basic information
Region (hg38): 19:12945855-12953642
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (28 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD23A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005053.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 26 | 27 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 26 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAD23A | protein_coding | protein_coding | ENST00000586534 | 9 | 7788 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.184 | 0.816 | 125733 | 0 | 7 | 125740 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 164 | 232 | 0.706 | 0.0000142 | 2343 |
| Missense in Polyphen | 23 | 65.146 | 0.35305 | 751 | ||
| Synonymous | 0.322 | 101 | 105 | 0.960 | 0.00000757 | 721 |
| Loss of Function | 3.06 | 5 | 19.6 | 0.255 | 0.00000100 | 219 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000916 | 0.0000910 |
| 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 | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome.; FUNCTION: (Microbial infection) Involved in Vpr-dependent replication of HIV-1 in non-proliferating cells and primary macrophages. Required for the association of HIV-1 Vpr with the host proteasome. {ECO:0000269|PubMed:20614012}.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Nucleotide Excision Repair ;DNA Repair;Josephin domain DUBs;Post-translational protein modification;Metabolism of proteins;Deubiquitination;DNA Damage Recognition in GG-NER;Formation of Incision Complex in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.199
Intolerance Scores
- loftool
- 0.464
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 75.29
Haploinsufficiency Scores
- pHI
- 0.758
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.440
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rad23a
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; normal 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);
Gene ontology
- Biological process
- nucleotide-excision repair;viral process;protein deubiquitination;protein destabilization;regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of viral genome replication;positive regulation of cell cycle
- Cellular component
- proteasome complex;nucleus;nucleoplasm;cytoplasm;microtubule organizing center;cytosol;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- damaged DNA binding;single-stranded DNA binding;protein binding;kinase binding;polyubiquitin modification-dependent protein binding;ubiquitin binding;proteasome binding;ubiquitin-specific protease binding