RPP25L

ribonuclease P/MRP subunit p25 like

Basic information

Region (hg38): 9:34610486-34612104

Previous symbols: [ "C9orf23" ]

Links

ENSG00000164967 ∙ NCBI:138716 ∙ ∙ HGNC:19909 ∙ Uniprot:Q8N5L8 ∙ 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 RPP25L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPP25L 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in RPP25L

This is a list of pathogenic ClinVar variants found in the RPP25L region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34610836-G-T		not specified	Uncertain significance (May 02, 2024)
9-34610879-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-34610915-G-C		not specified	Uncertain significance (Nov 21, 2022)
9-34610945-A-G		not specified	Uncertain significance (Feb 06, 2025)
9-34611002-C-G		not specified	Uncertain significance (Nov 24, 2024)
9-34611005-G-A		not specified	Uncertain significance (Nov 09, 2022)
9-34611034-C-T		not specified	Uncertain significance (Apr 15, 2024)
9-34611107-C-T		not specified	Uncertain significance (Apr 06, 2023)
9-34611122-C-G		not specified	Uncertain significance (Feb 24, 2025)
9-34611140-G-A		not specified	Uncertain significance (May 24, 2023)
9-34611184-T-C		not specified	Uncertain significance (Sep 26, 2024)
9-34611245-T-C		not specified	Uncertain significance (Feb 01, 2025)
9-34611283-C-T		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPP25L	protein_coding	protein_coding	ENST00000297613	1	1619

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.676	0.305	125630	0	7	125637	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.793	87	110	0.788	0.00000727	1016
Missense in Polyphen		28	38.02	0.73646		377
Synonymous	0.430	38	41.5	0.915	0.00000214	394
Loss of Function	1.78	0	3.68	0.00	2.42e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a component of ribonuclease P or MRP.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0847
• hipred: N
• hipred_score: 0.485
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpp25l

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding;protein binding