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

ENSG00000114767 ∙ NCBI:9136 ∙ OMIM:620013 ∙ HGNC:16829 ∙ Uniprot:O43818 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in RRP9

This is a list of pathogenic ClinVar variants found in the RRP9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-51933523-G-T		not specified	Uncertain significance (May 24, 2023)
3-51933750-C-A		not specified	Uncertain significance (May 21, 2024)
3-51934708-C-A		not specified	Uncertain significance (May 26, 2022)
3-51934708-C-T		not specified	Uncertain significance (Apr 12, 2023)
3-51934759-C-A		not specified	Uncertain significance (Oct 26, 2021)
3-51935239-T-C		not specified	Uncertain significance (Feb 10, 2022)
3-51935351-T-C		not specified	Uncertain significance (Oct 16, 2023)
3-51935420-A-G		not specified	Uncertain significance (Sep 29, 2023)
3-51935472-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-51935631-T-C		not specified	Uncertain significance (Jan 08, 2024)
3-51935644-C-T		not specified	Uncertain significance (Apr 04, 2024)
3-51936270-C-A		not specified	Uncertain significance (Jan 08, 2024)
3-51936280-T-G			Likely benign (Nov 01, 2022)
3-51936450-G-C		not specified	Uncertain significance (Feb 28, 2024)
3-51937264-T-C		not specified	Uncertain significance (May 17, 2023)
3-51937288-C-T		not specified	Likely benign (Dec 05, 2022)
3-51937290-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-51937580-G-C		not specified	Uncertain significance (May 27, 2022)
3-51937724-G-C		not specified	Uncertain significance (Feb 05, 2024)
3-51938103-C-A		not specified	Uncertain significance (Jan 23, 2024)
3-51941435-C-G		not specified	Uncertain significance (Feb 17, 2024)
3-51941824-G-A		not specified	Uncertain significance (Aug 16, 2021)
3-51941837-C-G		not specified	Uncertain significance (Jun 18, 2021)
3-51941839-C-A		not specified	Uncertain significance (Oct 05, 2021)
3-51941845-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rrp9

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