RRP8

ribosomal RNA processing 8, the group of eNoSC complex|Ribosomal biogenesis factors|7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 11:6595072-6603616

Previous symbols: [ "KIAA0409" ]

Links

ENSG00000132275 ∙ NCBI:23378 ∙ OMIM:615818 ∙ HGNC:29030 ∙ Uniprot:O43159 ∙ 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 RRP8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP8 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					1	1
missense			38	1	2	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	38	2	3

Variants in RRP8

This is a list of pathogenic ClinVar variants found in the RRP8 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6600196-C-G		not specified	Uncertain significance (Apr 12, 2022)
11-6600214-G-C		not specified	Uncertain significance (Jan 04, 2022)
11-6600270-G-A			Likely benign (May 09, 2018)
11-6600490-G-A		not specified	Uncertain significance (Nov 14, 2023)
11-6600496-A-G		not specified	Uncertain significance (Oct 04, 2022)
11-6600498-C-A		not specified	Uncertain significance (Sep 29, 2023)
11-6600505-C-T		not specified	Uncertain significance (Oct 27, 2022)
11-6600523-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-6600571-T-G		not specified	Uncertain significance (Feb 10, 2022)
11-6600781-G-A			Benign (May 08, 2018)
11-6600955-G-C		not specified	Uncertain significance (Jul 29, 2023)
11-6600993-C-T		not specified	Uncertain significance (Feb 02, 2022)
11-6600994-G-A		not specified	Uncertain significance (Feb 03, 2022)
11-6601041-A-T		not specified	Uncertain significance (Dec 22, 2023)
11-6601150-G-A			Likely benign (Nov 01, 2022)
11-6601168-C-T		not specified	Uncertain significance (Apr 25, 2023)
11-6601174-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-6601182-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-6601221-C-T		not specified	Uncertain significance (May 14, 2024)
11-6601222-G-A		not specified	Uncertain significance (Jul 08, 2022)
11-6601263-C-T		Autism spectrum disorder	association (-)
11-6601302-T-C		not specified	Uncertain significance (Aug 11, 2022)
11-6601317-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-6601332-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-6601343-G-A			Benign (May 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP8	protein_coding	protein_coding	ENST00000254605	7	8546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-10	0.182	125560	0	188	125748	0.000748

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	314	260	1.21	0.0000148	2945
Missense in Polyphen		97	91.778	1.0569		1045
Synonymous	-2.71	125	92.0	1.36	0.00000424	908
Loss of Function	0.631	17	20.0	0.848	0.00000109	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000991	0.000986
Ashkenazi Jewish	0.00182	0.00169
East Asian	0.000218	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00106	0.00102
Middle Eastern	0.000218	0.000217
South Asian	0.000719	0.000719
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone-modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at 'Lys- 9' (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus. In the complex, RRP8 binds to H3K9me2 and probably acts as a methyltransferase. Its substrates are however unknown. {ECO:0000269|PubMed:18485871}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;SIRT1 negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription) (Consensus)

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• loftool: 0.816
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.273
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp8
• 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: chromatin silencing at rDNA;rRNA processing;methylation;cellular response to glucose starvation;regulation of transcription by glucose;positive regulation of cell cycle arrest;intrinsic apoptotic signaling pathway by p53 class mediator
• Cellular component: nucleus;nucleoplasm;chromatin silencing complex;nucleolus;cytosol;plasma membrane;rDNA heterochromatin
• Molecular function: RNA binding;protein binding;S-adenosylmethionine-dependent methyltransferase activity;methylated histone binding