RRP15

ribosomal RNA processing 15 homolog, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 1:218285293-218337983

Previous symbols: [ "KIAA0507" ]

Links

ENSG00000067533 ∙ NCBI:51018 ∙ OMIM:611193 ∙ HGNC:24255 ∙ Uniprot:Q9Y3B9 ∙ 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 RRP15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP15 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			16			16
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in RRP15

This is a list of pathogenic ClinVar variants found in the RRP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-218285339-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-218285381-A-T		not specified	Uncertain significance (Aug 16, 2021)
1-218285410-G-T		not specified	Uncertain significance (Jun 07, 2023)
1-218285439-C-G		not specified	Uncertain significance (Feb 21, 2024)
1-218285440-A-C		not specified	Uncertain significance (Nov 03, 2022)
1-218285441-C-G		not specified	Uncertain significance (Feb 10, 2023)
1-218302369-A-T		not specified	Uncertain significance (May 27, 2022)
1-218302434-G-T		not specified	Uncertain significance (Apr 09, 2024)
1-218302471-A-G		not specified	Uncertain significance (Dec 21, 2021)
1-218302476-A-G		not specified	Uncertain significance (Jul 13, 2022)
1-218302482-A-T		not specified	Uncertain significance (Jan 19, 2024)
1-218302519-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-218305099-G-C		not specified	Uncertain significance (May 07, 2024)
1-218305100-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-218305111-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-218307433-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-218307520-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-218307594-G-A		not specified	Uncertain significance (May 28, 2024)
1-218330982-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-218330991-G-A		not specified	Uncertain significance (Nov 22, 2023)
1-218331050-G-T		not specified	Uncertain significance (Feb 22, 2023)
1-218331057-GC-G			Benign (Sep 09, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP15	protein_coding	protein_coding	ENST00000366932	5	52697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000294	0.812	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.453	167	151	1.10	0.00000728	1892
Missense in Polyphen		35	33.122	1.0567		491
Synonymous	-0.290	53	50.4	1.05	0.00000248	486
Loss of Function	1.17	7	11.2	0.623	4.68e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000615	0.000612
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.0000547	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.643
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.426
• hipred: Y
• hipred_score: 0.584
• ghis: 0.482

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp15

Gene ontology

• Biological process: rRNA processing
• Cellular component: preribosome, large subunit precursor