RPP38

ribonuclease P/MRP subunit p38

Basic information

Region (hg38): 10:15097179-15139818

Links

ENSG00000152464 ∙ NCBI:10557 ∙ OMIM:606116 ∙ HGNC:30329 ∙ Uniprot:P78345 ∙ 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 RPP38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPP38 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	1

Variants in RPP38

This is a list of pathogenic ClinVar variants found in the RPP38 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-15103343-G-A		not specified	Uncertain significance (Aug 16, 2022)
10-15103360-A-G		not specified	Uncertain significance (Jan 19, 2022)
10-15103389-G-C		not specified	Uncertain significance (Jan 25, 2024)
10-15103416-C-A		not specified	Uncertain significance (Aug 01, 2022)
10-15103429-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-15103441-T-G		not specified	Uncertain significance (Jan 23, 2023)
10-15103496-A-C		not specified	Uncertain significance (May 29, 2024)
10-15103544-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-15103604-C-G		not specified	Likely benign (Dec 01, 2022)
10-15103606-A-C		not specified	Uncertain significance (May 06, 2022)
10-15103616-T-C		not specified	Likely benign (Nov 17, 2023)
10-15103696-G-A		not specified	Uncertain significance (Oct 05, 2023)
10-15103714-G-T		not specified	Uncertain significance (Jun 28, 2022)
10-15103735-G-A		not specified	Uncertain significance (Jul 12, 2022)
10-15103761-G-T		not specified	Uncertain significance (Apr 12, 2022)
10-15103764-A-T		not specified	Uncertain significance (Aug 13, 2021)
10-15103801-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-15103804-C-T		not specified	Uncertain significance (Jun 05, 2024)
10-15103811-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-15103825-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-15103999-A-G		not specified	Uncertain significance (Apr 26, 2024)
10-15104060-G-C		not specified	Uncertain significance (Jan 23, 2023)
10-15104080-T-C			Benign (Feb 26, 2018)
10-15104151-A-T		not specified	Uncertain significance (Jan 08, 2024)
10-15109205-A-G		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPP38	protein_coding	protein_coding	ENST00000378197	1	42639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000201	0.502	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.217	166	158	1.05	0.00000880	1833
Missense in Polyphen		57	54.273	1.0502		613
Synonymous	-0.991	76	65.8	1.16	0.00000420	575
Loss of Function	0.378	6	7.09	0.847	2.97e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000894	0.0000894
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000264	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000392	0.000392
Other	0.000174	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. RPP38 may associate transiently with RNase P RNA as a factor involved in the transport of H1 RNA to the putative site of its assembly in the cell, the nucleolus.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human);Integrated Breast Cancer Pathway;tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.0848

Intolerance Scores

• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.0290
• hipred: N
• hipred_score: 0.376
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpp38

Gene ontology

• Biological process: tRNA processing;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: fibrillar center;nucleus;nucleoplasm;nucleolar ribonuclease P complex;nucleolus
• Molecular function: ribonuclease P activity;protein binding