RRN3

RRN3 homolog, RNA polymerase I transcription factor, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 16:15060033-15094311

Links

ENSG00000085721 ∙ NCBI:54700 ∙ OMIM:605121 ∙ HGNC:30346 ∙ Uniprot:Q9NYV6 ∙ 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 RRN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RRN3 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		2
missense			32	1	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	1

Variants in RRN3

This is a list of pathogenic ClinVar variants found in the RRN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15061779-G-A		not specified	Uncertain significance (Jun 29, 2022)
16-15061787-A-T		not specified	Uncertain significance (Mar 20, 2024)
16-15061845-C-T		not specified	Uncertain significance (Dec 15, 2022)
16-15061846-G-A			Likely benign (Feb 01, 2023)
16-15063237-T-G		not specified	Uncertain significance (Nov 27, 2023)
16-15065265-T-C		not specified	Uncertain significance (Aug 22, 2023)
16-15065283-A-G		not specified	Uncertain significance (Mar 01, 2023)
16-15065291-C-A		not specified	Uncertain significance (Jun 09, 2022)
16-15065317-C-A		not specified	Uncertain significance (Apr 25, 2023)
16-15068205-A-C		not specified	Uncertain significance (Oct 27, 2021)
16-15068232-C-G		not specified	Uncertain significance (Jan 16, 2024)
16-15068232-C-T		not specified	Uncertain significance (Mar 14, 2023)
16-15068273-C-G		not specified	Uncertain significance (Jun 05, 2024)
16-15070085-C-T		not specified	Uncertain significance (Jul 29, 2023)
16-15070105-C-T		not specified	Uncertain significance (May 06, 2024)
16-15070109-A-C		not specified	Uncertain significance (Jul 09, 2021)
16-15071206-C-A		not specified	Uncertain significance (May 23, 2024)
16-15073042-C-A		not specified	Uncertain significance (May 09, 2024)
16-15074810-C-A		not specified	Uncertain significance (Mar 30, 2022)
16-15076611-T-C		not specified	Likely benign (Feb 28, 2024)
16-15080027-G-C		not specified	Uncertain significance (May 23, 2024)
16-15080065-C-G		not specified	Uncertain significance (Jun 07, 2023)
16-15080083-T-A		not specified	Uncertain significance (May 20, 2024)
16-15080087-C-T		not specified	Uncertain significance (Oct 04, 2022)
16-15083524-C-T		not specified	Uncertain significance (Jun 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RRN3	protein_coding	protein_coding	ENST00000198767	18	34296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000162	1.00	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.770	381	341	1.12	0.0000179	4282
Missense in Polyphen		135	135.44	0.99672		1796
Synonymous	-2.32	159	126	1.26	0.00000685	1194
Loss of Function	3.15	14	33.8	0.414	0.00000166	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000271
Ashkenazi Jewish	0.000147	0.0000992
East Asian	0.000166	0.000163
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000175	0.000167
Middle Eastern	0.000166	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient transcription initiation by RNA polymerase I. Required for the formation of the competent preinitiation complex (PIC). Dissociates from pol I as a consequence of transcription. In vitro, cannot activate transcription in a subsequent transcription reaction (By similarity). {ECO:0000250, ECO:0000269|PubMed:10758157, ECO:0000269|PubMed:11250903, ECO:0000269|PubMed:11265758, ECO:0000269|PubMed:15805466}.
• Pathway: Gene expression (Transcription);RNA Polymerase I Promoter Clearance;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;mTOR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.768
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.0992
• hipred: Y
• hipred_score: 0.648
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.953

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrn3
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); embryo phenotype

Gene ontology

• Biological process: RNA polymerase I preinitiation complex assembly;in utero embryonic development;transcription initiation from RNA polymerase I promoter;nucleolus organization;cytoplasm organization;cell population proliferation;positive regulation of neuron projection development;ribosome biogenesis;positive regulation of transcription, DNA-templated;homeostasis of number of cells;negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator;regulation of DNA-templated transcription, initiation
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: RNA polymerase I core binding;RNA polymerase I CORE element sequence-specific DNA binding;RNA polymerase I general transcription initiation factor activity