RRP9

ribosomal RNA processing 9, U3 small nucleolar RNA binding protein, the group of Ribosomal biogenesis factors|U3 small nucleolar ribonucleoprotein|WD repeat domain containing

Basic information

Region (hg38): 3:51933429-51941904

Previous symbols: [ "RNU3IP2" ]

Links

ENSG00000114767NCBI:9136OMIM:620013HGNC:16829Uniprot:O43818AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RRP9 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
56
clinvar
2
clinvar
58
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 56 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RRP9protein_codingprotein_codingENST00000232888 158512
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2850.7151257290181257470.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.242372970.7980.00001833049
Missense in Polyphen69103.830.664551094
Synonymous0.07651151160.9910.00000706953
Loss of Function3.89730.00.2340.00000152323

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003380.000338
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00008880.0000879
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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