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.

• not_provided (2 variants)

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. These statistics are base on transcript: NM_000017793.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	0	2

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