RPP30

ribonuclease P/MRP subunit p30

Basic information

Region (hg38): 10:90871952-90908553

Links

ENSG00000148688 ∙ NCBI:10556 ∙ OMIM:606115 ∙ HGNC:17688 ∙ Uniprot:P78346 ∙ 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 RPP30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPP30 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
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in RPP30

This is a list of pathogenic ClinVar variants found in the RPP30 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-90871994-T-G		not specified	Uncertain significance (Jan 17, 2024)
10-90872018-C-T			Likely benign (Mar 01, 2023)
10-90872055-G-C		not specified	Uncertain significance (Jun 29, 2022)
10-90876069-G-A		not specified	Uncertain significance (Sep 14, 2023)
10-90876073-C-T		not specified	Uncertain significance (Mar 02, 2023)
10-90879130-T-C		not specified	Uncertain significance (Jan 18, 2023)
10-90885869-C-T		not specified	Uncertain significance (Jan 06, 2023)
10-90885887-C-T		not specified	Uncertain significance (Dec 13, 2022)
10-90894817-G-C		not specified	Uncertain significance (Jun 10, 2024)
10-90894835-A-G		not specified	Uncertain significance (Apr 22, 2022)
10-90894839-G-A		not specified	Uncertain significance (Apr 19, 2024)
10-90894845-A-G		not specified	Uncertain significance (Dec 16, 2023)
10-90894865-A-C		not specified	Uncertain significance (Apr 07, 2022)
10-90896315-G-A		not specified	Uncertain significance (Mar 13, 2023)
10-90896315-G-C		not specified	Uncertain significance (Sep 27, 2022)
10-90896344-G-A		not specified	Uncertain significance (Feb 23, 2023)
10-90896344-G-T		not specified	Uncertain significance (Feb 21, 2024)
10-90896374-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-90896378-C-T		not specified	Likely benign (Jan 26, 2022)
10-90896388-T-C			Likely benign (Mar 01, 2023)
10-90900589-T-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPP30	protein_coding	protein_coding	ENST00000413330	13	36840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.36e-8	0.648	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.758	188	161	1.17	0.00000796	2057
Missense in Polyphen		47	44.389	1.0588		589
Synonymous	-1.04	67	57.0	1.18	0.00000289	644
Loss of Function	1.19	14	19.7	0.711	0.00000101	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000381	0.000381
South Asian	0.000327	0.000327
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.
• 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: 0.249

Intolerance Scores

• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.281
• ghis: 0.616

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.130

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpp30

Gene ontology

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