RPP25

ribonuclease P and MRP subunit p25

Basic information

Region (hg38): 15:74954418-74956772

Links

ENSG00000178718 ∙ NCBI:54913 ∙ OMIM:619235 ∙ HGNC:30361 ∙ Uniprot:Q9BUL9 ∙ 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 RPP25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPP25 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					2	2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	2

Variants in RPP25

This is a list of pathogenic ClinVar variants found in the RPP25 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74956016-G-A		not specified	Uncertain significance (Nov 18, 2023)
15-74956051-G-C		not specified	Uncertain significance (Feb 22, 2023)
15-74956103-A-T		not specified	Uncertain significance (Apr 25, 2022)
15-74956109-C-T		not specified	Uncertain significance (Apr 09, 2024)
15-74956144-C-A		not specified	Uncertain significance (May 16, 2024)
15-74956169-G-A		not specified	Uncertain significance (Feb 21, 2024)
15-74956218-C-T			Benign (Jun 13, 2018)
15-74956224-G-T			Benign (Jun 23, 2018)
15-74956252-G-A		not specified	Uncertain significance (Apr 05, 2023)
15-74956259-G-T		not specified	Uncertain significance (Jan 24, 2023)
15-74956340-C-T		not specified	Uncertain significance (Dec 27, 2022)
15-74956370-G-A		not specified	Uncertain significance (Aug 09, 2021)
15-74956388-C-A		not specified	Uncertain significance (Jan 26, 2023)
15-74956447-A-G		not specified	Uncertain significance (Aug 02, 2023)
15-74956475-G-T		not specified	Uncertain significance (Nov 17, 2022)
15-74956499-C-T		not specified	Uncertain significance (Mar 25, 2024)
15-74956507-C-T		not specified	Uncertain significance (Mar 28, 2024)
15-74956532-C-T		not specified	Uncertain significance (Apr 04, 2024)
15-74956535-C-G		not specified	Uncertain significance (Apr 04, 2024)
15-74956535-C-T		not specified	Uncertain significance (Aug 21, 2023)
15-74956550-C-T		not specified	Uncertain significance (Feb 11, 2022)
15-74956572-G-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPP25	protein_coding	protein_coding	ENST00000322177	1	3049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.209	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.724	92	114	0.809	0.00000569	1225
Missense in Polyphen		38	52.764	0.72019		598
Synonymous	1.61	40	55.2	0.724	0.00000304	449
Loss of Function	1.03	1	2.90	0.345	1.25e-7	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP. This subunit binds to RNA.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.100

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.347
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpp25

Gene ontology

• Biological process: tRNA 5'-leader removal;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: ribonuclease MRP complex;nucleoplasm;microtubule organizing center;multimeric ribonuclease P complex
• Molecular function: RNA binding;ribonuclease P activity;protein binding