RRP12

ribosomal RNA processing 12 homolog, the group of Armadillo like helical domain containing|Ribosomal biogenesis factors

Basic information

Region (hg38): 10:97356357-97426076

Previous symbols: [ "KIAA0690" ]

Links

ENSG00000052749 ∙ NCBI:23223 ∙ OMIM:617723 ∙ HGNC:29100 ∙ Uniprot:Q5JTH9 ∙ 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 RRP12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRP12 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				2	1	3
missense			88	4	1	93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	88	6	2

Variants in RRP12

This is a list of pathogenic ClinVar variants found in the RRP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97357104-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-97357147-G-A		not specified	Uncertain significance (Mar 21, 2023)
10-97357167-T-C		not specified	Uncertain significance (Nov 09, 2022)
10-97357176-C-T		not specified	Uncertain significance (Dec 03, 2021)
10-97358541-G-A		not specified	Uncertain significance (Oct 03, 2022)
10-97358582-T-G		not specified	Uncertain significance (Oct 02, 2023)
10-97360562-T-C		not specified	Likely benign (Sep 25, 2023)
10-97360579-C-G		not specified	Uncertain significance (Sep 12, 2023)
10-97360589-T-A		not specified	Uncertain significance (Feb 13, 2024)
10-97360594-G-C		not specified	Uncertain significance (Dec 13, 2022)
10-97366141-C-T		not specified	Uncertain significance (Mar 07, 2023)
10-97366155-C-T		not specified	Likely benign (Mar 13, 2023)
10-97366230-G-A		not specified	Uncertain significance (Mar 20, 2024)
10-97366456-T-A		not specified	Uncertain significance (Apr 24, 2024)
10-97366466-T-C		not specified	Uncertain significance (Jun 09, 2022)
10-97366491-C-T		not specified	Uncertain significance (Mar 30, 2024)
10-97366532-C-T		not specified	Uncertain significance (Feb 14, 2023)
10-97366580-T-C		not specified	Uncertain significance (May 17, 2023)
10-97366581-T-C		not specified	Uncertain significance (Dec 09, 2023)
10-97366588-C-G		not specified	Uncertain significance (Jun 10, 2022)
10-97366615-C-A		not specified	Uncertain significance (Jan 23, 2023)
10-97366620-T-C		not specified	Uncertain significance (Nov 16, 2022)
10-97366800-C-T		not specified	Uncertain significance (Jan 07, 2022)
10-97366835-C-G		not specified	Uncertain significance (Aug 26, 2022)
10-97366835-C-T		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRP12	protein_coding	protein_coding	ENST00000370992	34	45013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.79e-11	1.00	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.772	714	774	0.922	0.0000466	8374
Missense in Polyphen		116	144.7	0.80165		1517
Synonymous	-1.94	364	320	1.14	0.0000199	2632
Loss of Function	4.49	30	70.8	0.424	0.00000375	801

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000485	0.000485
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000371	0.000369
Middle Eastern	0.000109	0.000109
South Asian	0.000165	0.000163
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• loftool: 0.755
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.66

Haploinsufficiency Scores

• pHI: 0.367
• hipred: Y
• hipred_score: 0.577
• ghis: 0.496

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrp12

Gene ontology

• Cellular component: nucleolus;integral component of membrane;nuclear membrane
• Molecular function: RNA binding