RRP1

ribosomal RNA processing 1, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 21:43789513-43805293

Links

ENSG00000160214 ∙ NCBI:8568 ∙ OMIM:610653 ∙ HGNC:18785 ∙ Uniprot:P56182 ∙ 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 RRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP1 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				3	1	4
missense			31	4	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	31	7	4

Variants in RRP1

This is a list of pathogenic ClinVar variants found in the RRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-43789675-C-T		not specified	Uncertain significance (Nov 27, 2024)
21-43789688-A-G		not specified	Uncertain significance (Aug 17, 2022)
21-43789710-G-A			Likely benign (Jul 30, 2018)
21-43789748-C-G		not specified	Uncertain significance (Mar 15, 2024)
21-43789759-G-T		not specified	Uncertain significance (Sep 09, 2024)
21-43791377-A-C		not specified	Uncertain significance (Dec 21, 2022)
21-43791411-G-A		not specified	Uncertain significance (Mar 22, 2023)
21-43793309-C-T			Benign (Jul 10, 2018)
21-43793321-C-T		not specified	Uncertain significance (Sep 09, 2024)
21-43793335-G-C		not specified	Uncertain significance (Feb 15, 2023)
21-43793336-G-A		not specified	Likely benign (Dec 04, 2024)
21-43793360-G-A		not specified	Uncertain significance (Oct 29, 2024)
21-43793367-C-T		not specified	Uncertain significance (Jan 05, 2022)
21-43793384-C-T		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
21-43793394-A-G		not specified	Uncertain significance (Mar 15, 2024)
21-43793402-A-G		not specified	Uncertain significance (Apr 19, 2023)
21-43797542-C-T			Likely benign (Mar 29, 2018)
21-43797550-A-C		not specified	Uncertain significance (Jun 21, 2023)
21-43797658-A-T		not specified	Uncertain significance (Nov 15, 2021)
21-43797676-A-G		not specified	Uncertain significance (Sep 06, 2022)
21-43797922-C-A		not specified	Uncertain significance (Nov 25, 2024)
21-43797948-C-T		not specified	Uncertain significance (Nov 10, 2022)
21-43797962-G-T		not specified	Uncertain significance (Aug 16, 2022)
21-43798012-G-C		not specified	Uncertain significance (Aug 12, 2024)
21-43798014-A-T		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP1	protein_coding	protein_coding	ENST00000497547	13	15781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000749	0.996	124799	0	17	124816	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.329	294	279	1.06	0.0000174	2978
Missense in Polyphen		68	80.049	0.84948		958
Synonymous	0.702	106	116	0.917	0.00000779	883
Loss of Function	2.55	11	24.7	0.446	0.00000130	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000197	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000556
Finnish	0.0000928	0.0000927
European (Non-Finnish)	0.0000893	0.0000883
Middle Eastern	0.0000562	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in the generation of 28S rRNA. {ECO:0000269|PubMed:10341208}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.649
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.36

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.531
• ghis: 0.496

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp1

Zebrafish Information Network

• Gene name: rrp1
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: atrophied

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleus;nucleolus;preribosome, large subunit precursor;preribosome, small subunit precursor
• Molecular function: RNA binding;protein binding