RAD23B
RAD23 homolog B, nucleotide excision repair protein, the group of Nucleotide excision repair
Basic information
Region (hg38): 9:107283136-107332192
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 RAD23B 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 | 3 | |||||
| missense | 19 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 4 | 0 |
Variants in RAD23B
This is a list of pathogenic ClinVar variants found in the RAD23B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-107283642-C-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 9-107300187-C-G | not specified | Uncertain significance (Feb 07, 2023) | ||
| 9-107306389-T-G | not specified | Uncertain significance (Aug 04, 2023) | ||
| 9-107306458-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 9-107306532-C-T | not specified | Uncertain significance (May 08, 2023) | ||
| 9-107306577-G-A | not specified | Likely benign (Jan 02, 2024) | ||
| 9-107306580-A-G | not specified | Uncertain significance (Nov 07, 2022) | ||
| 9-107306601-A-G | RAD23B-related disorder | Uncertain significance (Aug 31, 2023) | ||
| 9-107306603-G-A | RAD23B-related disorder | Likely benign (Apr 08, 2021) | ||
| 9-107306631-C-T | not specified | Uncertain significance (Feb 13, 2024) | ||
| 9-107311687-C-T | RAD23B-related disorder • not specified | Uncertain significance (Feb 08, 2024) | ||
| 9-107311693-A-G | not specified | Uncertain significance (Mar 24, 2023) | ||
| 9-107318823-G-T | not specified | Uncertain significance (Jan 17, 2024) | ||
| 9-107318849-C-T | RAD23B-related disorder | Likely benign (Jan 25, 2021) | ||
| 9-107318853-G-C | not specified | Uncertain significance (Feb 06, 2023) | ||
| 9-107322003-A-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 9-107322035-C-T | not specified | Uncertain significance (Nov 02, 2021) | ||
| 9-107322049-C-T | not specified | Uncertain significance (Oct 29, 2021) | ||
| 9-107322056-C-G | not specified | Uncertain significance (Jan 24, 2023) | ||
| 9-107322094-A-G | not specified | Uncertain significance (May 24, 2023) | ||
| 9-107322105-A-G | RAD23B-related disorder | Likely benign (Jul 01, 2024) | ||
| 9-107323995-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 9-107324898-G-A | not specified | Uncertain significance (Jun 08, 2022) | ||
| 9-107329543-T-C | not specified | Likely benign (Feb 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAD23B | protein_coding | protein_coding | ENST00000358015 | 10 | 49058 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00370 | 125696 | 0 | 1 | 125697 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.75 | 138 | 209 | 0.659 | 0.00000985 | 2634 |
| Missense in Polyphen | 10 | 57.613 | 0.17357 | 742 | ||
| Synonymous | -0.814 | 82 | 73.1 | 1.12 | 0.00000379 | 821 |
| Loss of Function | 4.04 | 1 | 20.9 | 0.0478 | 0.00000105 | 252 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 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. May play a role in endoplasmic reticulum- associated degradation (ERAD) of misfolded glycoproteins by association with PNGase and delivering deglycosylated proteins to the proteasome.; FUNCTION: The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, XPA, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single-stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. XPC:RAD23B induces a bend in DNA upon binding. XPC:RAD23B stimulates the activity of DNA glycosylases TDG and SMUG1.;
- Pathway
- Nucleotide excision repair - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;DNA Repair;Josephin domain DUBs;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;Deubiquitination;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;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
- 0.243
Intolerance Scores
- loftool
- 0.412
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.57
Haploinsufficiency Scores
- pHI
- 0.623
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rad23b
- 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; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial 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); reproductive system phenotype; 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- nucleotide-excision repair, DNA damage recognition;nucleotide-excision repair;nucleotide-excision repair, preincision complex assembly;protein folding;spermatogenesis;protein deubiquitination;regulation of proteasomal ubiquitin-dependent protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;embryonic organ development;global genome nucleotide-excision repair;cellular response to interleukin-7
- Cellular component
- proteasome complex;nucleus;nucleoplasm;cytosol;XPC complex
- Molecular function
- damaged DNA binding;single-stranded DNA binding;protein binding;polyubiquitin modification-dependent protein binding;ubiquitin binding;proteasome binding