RPF2

ribosome production factor 2 homolog

Basic information

Region (hg38): 6:110982015-111028263

Previous symbols: [ "BXDC1" ]

Links

ENSG00000197498 ∙ NCBI:84154 ∙ OMIM:618471 ∙ HGNC:20870 ∙ Uniprot:Q9H7B2 ∙ 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 RPF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPF2 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			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	1

Variants in RPF2

This is a list of pathogenic ClinVar variants found in the RPF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-110982113-A-G		not specified	Likely benign (Oct 06, 2021)
6-110985036-C-G		not specified	Uncertain significance (Sep 06, 2022)
6-110985068-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-110985097-G-A		not specified	Uncertain significance (Dec 14, 2023)
6-110985125-T-C		not specified	Uncertain significance (Dec 07, 2024)
6-110989049-G-A			Benign (Feb 09, 2018)
6-110997243-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-110999713-C-T		not specified	Uncertain significance (Sep 26, 2024)
6-110999726-A-G		not specified	Uncertain significance (Jul 31, 2024)
6-111008077-T-C		not specified	Uncertain significance (Dec 21, 2023)
6-111008086-G-A		not specified	Uncertain significance (Nov 06, 2024)
6-111008099-T-G		not specified	Uncertain significance (Jun 12, 2023)
6-111008113-A-G		not specified	Uncertain significance (Feb 16, 2023)
6-111008116-A-G		not specified	Uncertain significance (Dec 04, 2024)
6-111008126-G-A		not specified	Uncertain significance (Sep 03, 2024)
6-111015777-T-C		not specified	Uncertain significance (Nov 30, 2022)
6-111015787-G-A		not specified	Uncertain significance (Dec 26, 2023)
6-111015804-T-G		not specified	Uncertain significance (Mar 31, 2023)
6-111015831-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-111024217-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-111024226-T-A		not specified	Uncertain significance (Aug 05, 2024)
6-111024239-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-111025419-A-G		not specified	Uncertain significance (Jul 25, 2023)
6-111025421-A-G		not specified	Uncertain significance (Jun 05, 2023)
6-111025430-G-T		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPF2	protein_coding	protein_coding	ENST00000441448	10	46249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0464	0.949	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.536	138	157	0.879	0.00000778	2000
Missense in Polyphen		41	42.923	0.95519		619
Synonymous	-0.381	61	57.3	1.06	0.00000302	546
Loss of Function	2.48	5	15.5	0.322	7.18e-7	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000719	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus. {ECO:0000269|PubMed:24120868}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.675
• hipred: Y
• hipred_score: 0.783
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpf2

Gene ontology

• Biological process: ribosomal large subunit assembly;maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);ribosomal large subunit biogenesis;regulation of signal transduction by p53 class mediator;protein localization to nucleolus
• Cellular component: nucleus;nucleolus
• Molecular function: RNA binding;5S rRNA binding