RPP40

ribonuclease P/MRP subunit p40

Basic information

Region (hg38): 6:4994717-5004063

Previous symbols: [ "RNASEP1" ]

Links

ENSG00000124787 ∙ NCBI:10799 ∙ OMIM:606117 ∙ HGNC:20992 ∙ Uniprot:O75818 ∙ 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 RPP40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPP40 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			13	1		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	13	1	0

Variants in RPP40

This is a list of pathogenic ClinVar variants found in the RPP40 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-4995175-C-T		not specified	Likely benign (Dec 22, 2023)
6-4995251-C-G		not specified	Uncertain significance (Oct 04, 2022)
6-4996003-T-C		not specified	Uncertain significance (Apr 25, 2022)
6-4996241-C-T		not specified	Uncertain significance (Jan 31, 2024)
6-4996274-G-C		not specified	Uncertain significance (Mar 04, 2024)
6-4996308-G-T		not specified	Uncertain significance (Dec 22, 2023)
6-4996315-A-C		not specified	Uncertain significance (Mar 19, 2024)
6-4996344-G-T		not specified	Uncertain significance (Dec 06, 2021)
6-4996408-G-A		not specified	Uncertain significance (May 12, 2024)
6-4998767-T-C		not specified	Uncertain significance (May 29, 2024)
6-4998790-T-C		not specified	Uncertain significance (Feb 03, 2022)
6-4999818-T-C		not specified	Uncertain significance (Aug 02, 2021)
6-4999871-T-C		not specified	Uncertain significance (May 10, 2024)
6-5002104-T-C		not specified	Uncertain significance (Oct 25, 2023)
6-5002119-T-G		not specified	Uncertain significance (Sep 07, 2022)
6-5002173-A-C		not specified	Uncertain significance (Apr 15, 2024)
6-5002182-T-C		not specified	Uncertain significance (Dec 19, 2022)
6-5002211-G-A		not specified	Uncertain significance (May 29, 2024)
6-5003915-G-C		not specified	Uncertain significance (Dec 15, 2023)
6-5003993-G-C		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPP40	protein_coding	protein_coding	ENST00000380051	8	9332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000131	0.963	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.240	180	189	0.951	0.00000923	2372
Missense in Polyphen		53	61.678	0.8593		814
Synonymous	-0.246	79	76.3	1.04	0.00000416	661
Loss of Function	1.87	9	17.4	0.517	7.96e-7	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
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: 0.100

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.0960
• hipred: N
• hipred_score: 0.319
• ghis: 0.444

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpp40

Gene ontology

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