RPRD1B
Basic information
Region (hg38): 20:38033725-38127780
Previous symbols: [ "C20orf77" ]
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 RPRD1B 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 | 4 | |||||
| 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 | 0 | 0 |
Variants in RPRD1B
This is a list of pathogenic ClinVar variants found in the RPRD1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-38033964-A-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 20-38048372-A-T | not specified | Uncertain significance (Mar 25, 2022) | ||
| 20-38057588-G-C | not specified | Uncertain significance (Feb 10, 2023) | ||
| 20-38059430-A-C | not specified | Uncertain significance (Sep 14, 2023) | ||
| 20-38066191-C-T | not specified | Uncertain significance (May 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPRD1B | protein_coding | protein_coding | ENST00000373433 | 7 | 58821 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0418 | 0.957 | 125737 | 0 | 9 | 125746 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.10 | 100 | 179 | 0.559 | 0.00000952 | 2093 |
| Missense in Polyphen | 7 | 52.728 | 0.13276 | 631 | ||
| Synonymous | -0.0383 | 73 | 72.6 | 1.01 | 0.00000371 | 648 |
| Loss of Function | 2.85 | 6 | 19.6 | 0.306 | 0.00000119 | 213 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000101 | 0.000101 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.0000927 | 0.0000924 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3' end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation. {ECO:0000269|PubMed:22231121, ECO:0000269|PubMed:22264791, ECO:0000269|PubMed:24399136, ECO:0000269|PubMed:24997600}.;
- Pathway
- Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.265
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.304
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.693
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.934
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rprd1b
- Phenotype
- hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- rprd1b
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- positive regulation of cell population proliferation;regulation of cell cycle process;mRNA 3'-end processing;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;dephosphorylation of RNA polymerase II C-terminal domain
- Cellular component
- nucleus;nucleoplasm;centrosome;cytosol;RNA polymerase II, holoenzyme
- Molecular function
- RNA polymerase II complex binding;protein binding;identical protein binding