RPF2

ribosome production factor 2 homolog

Basic information

Region (hg38): 6:110982015-111028263

Previous symbols: [ "BXDC1" ]

Links

ENSG00000197498NCBI:84154OMIM:618471HGNC:20870Uniprot:Q9H7B2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
1
clinvar
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)2373025
6-110985036-C-G not specified Uncertain significance (Sep 06, 2022)2310043
6-110985068-A-G not specified Uncertain significance (Sep 20, 2023)3155977
6-110985097-G-A not specified Uncertain significance (Dec 14, 2023)3155971
6-110985125-T-C not specified Uncertain significance (Dec 07, 2024)3435078
6-110989049-G-A Benign (Feb 09, 2018)776145
6-110997243-C-T not specified Uncertain significance (Oct 26, 2021)2257076
6-110999713-C-T not specified Uncertain significance (Sep 26, 2024)3435071
6-110999726-A-G not specified Uncertain significance (Jul 31, 2024)3155972
6-111008077-T-C not specified Uncertain significance (Dec 21, 2023)3155973
6-111008086-G-A not specified Uncertain significance (Nov 06, 2024)3435075
6-111008099-T-G not specified Uncertain significance (Jun 12, 2023)2559557
6-111008113-A-G not specified Uncertain significance (Feb 16, 2023)2463253
6-111008116-A-G not specified Uncertain significance (Dec 04, 2024)3435077
6-111008126-G-A not specified Uncertain significance (Sep 03, 2024)3435073
6-111015777-T-C not specified Uncertain significance (Nov 30, 2022)2330065
6-111015787-G-A not specified Uncertain significance (Dec 26, 2023)3155974
6-111015804-T-G not specified Uncertain significance (Mar 31, 2023)2531869
6-111015831-G-A not specified Uncertain significance (Jun 06, 2023)2557390
6-111024217-C-T not specified Uncertain significance (Sep 13, 2023)2623547
6-111024226-T-A not specified Uncertain significance (Aug 05, 2024)3435072
6-111024239-G-A not specified Uncertain significance (Sep 20, 2023)3155975
6-111025419-A-G not specified Uncertain significance (Jul 25, 2023)2613707
6-111025421-A-G not specified Uncertain significance (Jun 05, 2023)2556733
6-111025430-G-T not specified Uncertain significance (Mar 31, 2024)3315147

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPF2protein_codingprotein_codingENST00000441448 1046249
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04640.9491257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5361381570.8790.000007782000
Missense in Polyphen4142.9230.95519619
Synonymous-0.3816157.31.060.00000302546
Loss of Function2.48515.50.3227.18e-7230

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001770.000177
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0001390.000139
European (Non-Finnish)0.00007190.0000703
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001690.000163

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpf2
Phenotype

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