RPF1

ribosome production factor 1 homolog

Basic information

Region (hg38): 1:84479259-84498352

Previous symbols: [ "BXDC5" ]

Links

ENSG00000117133 ∙ NCBI:80135 ∙ ∙ HGNC:30350 ∙ Uniprot:Q9H9Y2 ∙ 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 RPF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPF1 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in RPF1

This is a list of pathogenic ClinVar variants found in the RPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-84479295-G-A		not specified	Uncertain significance (Feb 26, 2025)
1-84479295-G-T		not specified	Uncertain significance (May 24, 2023)
1-84479315-G-A		not specified	Uncertain significance (Jul 30, 2024)
1-84479315-G-T		not specified	Likely benign (Feb 04, 2025)
1-84479320-G-C		not specified	Uncertain significance (Feb 12, 2025)
1-84479325-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-84479333-C-T		not specified	Uncertain significance (Dec 17, 2023)
1-84479351-G-A		not specified	Uncertain significance (Jul 26, 2022)
1-84479354-C-T		not specified	Uncertain significance (Dec 05, 2022)
1-84479388-C-T		not specified	Uncertain significance (Jan 24, 2024)
1-84479397-G-A		not specified	Uncertain significance (Oct 12, 2024)
1-84479400-T-C		not specified	Uncertain significance (Oct 08, 2024)
1-84479412-A-G		not specified	Uncertain significance (Feb 07, 2025)
1-84479476-A-C		not specified	Uncertain significance (Dec 04, 2024)
1-84479478-T-C		not specified	Uncertain significance (Feb 13, 2024)
1-84479496-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-84479508-A-C		not specified	Uncertain significance (Dec 20, 2022)
1-84482972-A-G		not specified	Uncertain significance (Nov 09, 2024)
1-84482987-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-84489640-A-G		not specified	Uncertain significance (Sep 22, 2022)
1-84489649-C-G		not specified	Uncertain significance (Mar 21, 2024)
1-84489651-A-G		not specified	Uncertain significance (Jul 15, 2021)
1-84489664-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-84489718-G-A		not specified	Uncertain significance (Oct 04, 2024)
1-84490323-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPF1	protein_coding	protein_coding	ENST00000370654	9	18532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-8	0.475	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.195	187	195	0.961	0.0000101	2286
Missense in Polyphen		45	61.805	0.7281		743
Synonymous	-0.143	68	66.5	1.02	0.00000314	652
Loss of Function	0.942	14	18.4	0.763	9.49e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000734	0.000732
Ashkenazi Jewish	0.000447	0.000397
East Asian	0.000221	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000421	0.000413
Middle Eastern	0.000221	0.000217
South Asian	0.000336	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for ribosome biogenesis. {ECO:0000269|PubMed:11864606}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 1
• rvis_percentile_EVS: 90.65

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.680
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpf1

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleolus;preribosome, large subunit precursor
• Molecular function: RNA binding;protein binding