POP4

POP4 homolog, ribonuclease P/MRP subunit

Basic information

Region (hg38): 19:29606283-29617237

Links

ENSG00000105171 ∙ NCBI:10775 ∙ OMIM:606114 ∙ HGNC:30081 ∙ Uniprot:O95707 ∙ 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 POP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POP4 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	19	3	0

Variants in POP4

This is a list of pathogenic ClinVar variants found in the POP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-29608657-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-29610428-C-A		not specified	Uncertain significance (Mar 26, 2024)
19-29610464-C-G		not specified	Uncertain significance (Sep 25, 2023)
19-29610464-C-T		not specified	Likely benign (Mar 22, 2023)
19-29610466-C-T		not specified	Uncertain significance (Mar 07, 2025)
19-29610470-G-A		not specified	Likely benign (Mar 01, 2023)
19-29610493-G-A		not specified	Uncertain significance (Dec 30, 2024)
19-29610506-G-T		not specified	Uncertain significance (Oct 04, 2022)
19-29610529-T-G		not specified	Uncertain significance (Nov 20, 2024)
19-29610533-C-T		not specified	Uncertain significance (Jul 02, 2024)
19-29610555-G-T		not specified	Uncertain significance (Aug 08, 2022)
19-29610586-C-G		not specified	Uncertain significance (May 28, 2024)
19-29610587-A-C		not specified	Uncertain significance (Oct 06, 2021)
19-29610602-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-29611896-A-G		not specified	Uncertain significance (Nov 15, 2024)
19-29611905-A-C		not specified	Uncertain significance (Jan 26, 2023)
19-29612155-A-T		not specified	Uncertain significance (Sep 01, 2024)
19-29612163-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-29615246-A-T		not specified	Likely benign (Aug 12, 2021)
19-29615325-G-A		not specified	Uncertain significance (Dec 25, 2024)
19-29615325-G-C		not specified	Uncertain significance (Feb 25, 2025)
19-29615336-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-29615337-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-29615355-A-C		not specified	Uncertain significance (Jul 30, 2024)
19-29615363-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POP4	protein_coding	protein_coding	ENST00000585603	7	13221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000182	0.704	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.132	129	133	0.968	0.00000837	1424
Missense in Polyphen		26	36.785	0.70681		450
Synonymous	-0.773	61	53.8	1.13	0.00000341	410
Loss of Function	1.03	9	13.0	0.693	6.50e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000164	0.000163
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. May function with RPP38 to coordinate the nucleolar targeting and/or assembly of RNase P.
• 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: 0.125

Intolerance Scores

• loftool: 0.405
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.255
• hipred: N
• hipred_score: 0.376
• ghis: 0.579

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pop4
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; homeostasis/metabolism phenotype

Gene ontology

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