RRP1B

ribosomal RNA processing 1B, the group of Ribosomal biogenesis factors|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 21:43659560-43696079

Previous symbols: [ "KIAA0179" ]

Links

ENSG00000160208 ∙ NCBI:23076 ∙ OMIM:610654 ∙ HGNC:23818 ∙ Uniprot:Q14684 ∙ 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 RRP1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP1B 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				1	1	2
missense			32	4	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	32	5	2

Variants in RRP1B

This is a list of pathogenic ClinVar variants found in the RRP1B region.

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

Position	Type	Phenotype	Significance	ClinVar
21-43659750-A-G		not specified	Likely benign (Feb 28, 2023)
21-43669895-C-G		not specified	Uncertain significance (Jul 20, 2021)
21-43672340-C-T			Benign (Jun 26, 2018)
21-43672360-C-T		not specified	Conflicting classifications of pathogenicity (Jun 10, 2024)
21-43673912-A-G		not specified	Uncertain significance (Mar 15, 2024)
21-43673941-G-A		not specified	Uncertain significance (Dec 17, 2023)
21-43674628-T-A			Benign (Dec 31, 2019)
21-43674678-C-G		not specified	Uncertain significance (Dec 20, 2021)
21-43676759-G-A		not specified	Uncertain significance (Sep 06, 2022)
21-43676810-C-T		not specified	Uncertain significance (Jun 27, 2023)
21-43676866-C-A		not specified	Uncertain significance (Nov 21, 2022)
21-43676890-A-G		not specified	Uncertain significance (Jan 04, 2022)
21-43676903-A-G		not specified	Uncertain significance (May 29, 2024)
21-43683324-G-A		not specified	Uncertain significance (Mar 28, 2023)
21-43684629-G-A		not specified	Uncertain significance (Oct 13, 2023)
21-43684646-A-C		not specified	Uncertain significance (Apr 07, 2022)
21-43685777-G-A		not specified	Uncertain significance (Nov 03, 2022)
21-43685777-G-T		not specified	Uncertain significance (Dec 01, 2022)
21-43686809-A-C		not specified	Uncertain significance (May 13, 2024)
21-43686859-C-A		not specified	Uncertain significance (Jan 04, 2022)
21-43687534-T-C		not specified	Likely benign (Apr 01, 2024)
21-43687590-A-C		not specified	Uncertain significance (Aug 12, 2021)
21-43687615-C-G		not specified	Uncertain significance (Oct 25, 2023)
21-43687680-C-G		not specified	Uncertain significance (Dec 27, 2023)
21-43687777-T-C		not specified	Likely benign (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP1B	protein_coding	protein_coding	ENST00000340648	16	36530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-9	0.996	125700	1	47	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	334	413	0.808	0.0000225	4960
Missense in Polyphen		79	115.62	0.68329		1546
Synonymous	-0.390	172	166	1.04	0.00000968	1462
Loss of Function	2.63	20	37.3	0.536	0.00000212	435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000466	0.000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000262	0.000229
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates DNA damage-induced apoptosis by acting as a transcriptional coactivator of proapoptotic target genes of the transcriptional activator E2F1 (PubMed:20040599). Likely to play a role in ribosome biogenesis by targeting serine/threonine protein phosphatase PP1 to the nucleolus (PubMed:20926688). Involved in regulation of mRNA splicing (By similarity). Inhibits SIPA1 GTPase activity (By similarity). Involved in regulating expression of extracellular matrix genes (By similarity). Associates with chromatin and may play a role in modulating chromatin structure (PubMed:19710015). {ECO:0000250|UniProtKB:Q91YK2, ECO:0000269|PubMed:19710015, ECO:0000269|PubMed:20040599, ECO:0000269|PubMed:20926688}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.439
• hipred: Y
• hipred_score: 0.620
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp1b

Gene ontology

• Biological process: rRNA processing;mRNA processing;apoptotic process;RNA splicing;negative regulation of phosphatase activity;negative regulation of GTPase activity;positive regulation of apoptotic process;regulation of RNA splicing;positive regulation by host of viral transcription;positive regulation of transcription by RNA polymerase II;cellular response to virus
• Cellular component: euchromatin;heterochromatin;granular component;nucleus;nucleoplasm;nucleolus;cytosol;preribosome, large subunit precursor;preribosome, small subunit precursor
• Molecular function: transcription coactivator activity;RNA binding;protein binding