POLR3F

RNA polymerase III subunit F, the group of RNA polymerase subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 20:18466878-18484648

Links

ENSG00000132664 ∙ NCBI:10621 ∙ OMIM:617455 ∙ HGNC:15763 ∙ Uniprot:Q9H1D9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 101 (varicella zoster virus-specific) (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 101 (varicella zoster virus-specific)	AD	Allergy/Immunology/Infectious	The condition involves susceptibility to sequelae of varicella infection, and acycloviri has been described as beneficial	Allergy/Immunology/Infectious	30211253

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POLR3F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR3F 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			15	9	4	28
missense			46		1	47
nonsense			2			2
start loss						0
frameshift			4			4
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region			10	5	1	16
non coding			13	10	11	34
Total	0	0	81	20	16

Variants in POLR3F

This is a list of pathogenic ClinVar variants found in the POLR3F region.

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

Position	Type	Phenotype	Significance	ClinVar
20-18467435-C-A		not specified	Benign (Jan 24, 2024)
20-18468987-C-G		not specified	Uncertain significance (Dec 20, 2023)
20-18468994-T-C		not specified	Uncertain significance (Oct 05, 2023)
20-18469014-A-G			Uncertain significance (Aug 10, 2023)
20-18469015-T-C			Uncertain significance (Jan 19, 2023)
20-18469030-G-A		not specified	Uncertain significance (Apr 08, 2024)
20-18469041-A-G			Uncertain significance (Jun 16, 2023)
20-18469065-A-G			Uncertain significance (Jul 07, 2023)
20-18469079-A-G			Uncertain significance (Jul 27, 2023)
20-18472828-G-A			Likely benign (Dec 22, 2023)
20-18472846-A-G			Uncertain significance (Nov 21, 2023)
20-18472867-A-G		not specified	Uncertain significance (Dec 10, 2023)
20-18472869-A-T			Uncertain significance (Aug 02, 2023)
20-18472870-C-T			Uncertain significance (Jul 26, 2023)
20-18472888-T-A			Uncertain significance (Jul 20, 2023)
20-18472891-A-G			Uncertain significance (Sep 21, 2023)
20-18472895-C-T			Uncertain significance (Mar 23, 2023)
20-18472906-C-G		not specified	Uncertain significance (Feb 27, 2023)
20-18472909-G-A			Uncertain significance (Jan 06, 2023)
20-18472916-A-G			Likely benign (Nov 13, 2023)
20-18472920-G-T			Likely benign (Dec 07, 2023)
20-18472920-GT-G			Benign (Jan 19, 2023)
20-18473379-A-G			Uncertain significance (Aug 10, 2022)
20-18473383-C-T			Likely benign (Jan 18, 2024)
20-18473387-A-G			Uncertain significance (May 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR3F	protein_coding	protein_coding	ENST00000377603	9	17517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000104	0.798	125644	0	103	125747	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	109	169	0.644	0.00000833	2085
Missense in Polyphen		19	43.056	0.44128		547
Synonymous	1.11	49	60.0	0.817	0.00000300	550
Loss of Function	1.35	12	18.2	0.658	8.69e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00633	0.00537
East Asian	0.000116	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000262	0.000255
Middle Eastern	0.000116	0.000109
South Asian	0.0000653	0.0000653
Other	0.00121	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway. Preferentially binds double-stranded DNA (dsDNA) (PubMed:21358628). {ECO:0000269|PubMed:19609254, ECO:0000269|PubMed:19631370, ECO:0000269|PubMed:21358628}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Cytosolic DNA-sensing pathway - Homo sapiens (human);RNA polymerase - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Pyrimidine metabolism;Gene expression (Transcription);Purine metabolism;Pyrimidine metabolism;RNA Polymerase III Transcription Termination;RNA Polymerase III Chain Elongation;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 1 Promoter;RNA Polymerase III Transcription Initiation From Type 2 Promoter;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.202
• hipred: Y
• hipred_score: 0.765
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr3f
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: polr3f
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: regulation of transcription by RNA polymerase III;transcription by RNA polymerase III;positive regulation of interferon-beta production;innate immune response;positive regulation of innate immune response;defense response to virus
• Cellular component: nucleoplasm;RNA polymerase III complex;cytosol
• Molecular function: RNA polymerase III activity;double-stranded DNA binding;DNA-directed 5'-3' RNA polymerase activity;protein binding