RPF2
Basic information
Region (hg38): 6:110982015-111028263
Previous symbols: [ "BXDC1" ]
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 RPF2 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 | 29 | 31 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 29 | 1 | 1 |
Variants in RPF2
This is a list of pathogenic ClinVar variants found in the RPF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-110982113-A-G | not specified | Likely benign (Oct 06, 2021) | ||
6-110985036-C-G | not specified | Uncertain significance (Sep 06, 2022) | ||
6-110985068-A-G | not specified | Uncertain significance (Sep 20, 2023) | ||
6-110985097-G-A | not specified | Uncertain significance (Dec 14, 2023) | ||
6-110985125-T-C | not specified | Uncertain significance (Dec 07, 2024) | ||
6-110989049-G-A | Benign (Feb 09, 2018) | |||
6-110997243-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
6-110999713-C-T | not specified | Uncertain significance (Sep 26, 2024) | ||
6-110999726-A-G | not specified | Uncertain significance (Jul 31, 2024) | ||
6-111008077-T-C | not specified | Uncertain significance (Dec 21, 2023) | ||
6-111008086-G-A | not specified | Uncertain significance (Nov 06, 2024) | ||
6-111008099-T-G | not specified | Uncertain significance (Jun 12, 2023) | ||
6-111008113-A-G | not specified | Uncertain significance (Feb 16, 2023) | ||
6-111008116-A-G | not specified | Uncertain significance (Dec 04, 2024) | ||
6-111008126-G-A | not specified | Uncertain significance (Sep 03, 2024) | ||
6-111015777-T-C | not specified | Uncertain significance (Nov 30, 2022) | ||
6-111015787-G-A | not specified | Uncertain significance (Dec 26, 2023) | ||
6-111015804-T-G | not specified | Uncertain significance (Mar 31, 2023) | ||
6-111015831-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
6-111024217-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
6-111024226-T-A | not specified | Uncertain significance (Aug 05, 2024) | ||
6-111024239-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
6-111025419-A-G | not specified | Uncertain significance (Jul 25, 2023) | ||
6-111025421-A-G | not specified | Uncertain significance (Jun 05, 2023) | ||
6-111025430-G-T | not specified | Uncertain significance (Mar 31, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPF2 | protein_coding | protein_coding | ENST00000441448 | 10 | 46249 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0464 | 0.949 | 125730 | 0 | 18 | 125748 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.536 | 138 | 157 | 0.879 | 0.00000778 | 2000 |
Missense in Polyphen | 41 | 42.923 | 0.95519 | 619 | ||
Synonymous | -0.381 | 61 | 57.3 | 1.06 | 0.00000302 | 546 |
Loss of Function | 2.48 | 5 | 15.5 | 0.322 | 7.18e-7 | 230 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000177 | 0.000177 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.0000719 | 0.0000703 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.000169 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus. {ECO:0000269|PubMed:24120868}.;
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.51
Haploinsufficiency Scores
- pHI
- 0.675
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpf2
- Phenotype
Gene ontology
- Biological process
- ribosomal large subunit assembly;maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);ribosomal large subunit biogenesis;regulation of signal transduction by p53 class mediator;protein localization to nucleolus
- Cellular component
- nucleus;nucleolus
- Molecular function
- RNA binding;5S rRNA binding