RRP9
Basic information
Region (hg38): 3:51933429-51941904
Previous symbols: [ "RNU3IP2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (57 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004704.5. 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 | 0 | |||||
missense | 56 | 58 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 56 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RRP9 | protein_coding | protein_coding | ENST00000232888 | 15 | 8512 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.285 | 0.715 | 125729 | 0 | 18 | 125747 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.24 | 237 | 297 | 0.798 | 0.0000183 | 3049 |
Missense in Polyphen | 69 | 103.83 | 0.66455 | 1094 | ||
Synonymous | 0.0765 | 115 | 116 | 0.991 | 0.00000706 | 953 |
Loss of Function | 3.89 | 7 | 30.0 | 0.234 | 0.00000152 | 323 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000338 | 0.000338 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000888 | 0.0000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA.;
- Pathway
- rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol
(Consensus)
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- loftool
- 0.369
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 42.06
Haploinsufficiency Scores
- pHI
- 0.814
- hipred
- Y
- hipred_score
- 0.563
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.910
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rrp9
- Phenotype
Gene ontology
- Biological process
- rRNA processing
- Cellular component
- nucleoplasm;nucleolus;box C/D snoRNP complex;small-subunit processome
- Molecular function
- RNA binding;U3 snoRNA binding