POLR3E

RNA polymerase III subunit E, the group of RNA polymerase subunits

Basic information

Region (hg38): 16:22297375-22335101

Links

ENSG00000058600 ∙ NCBI:55718 ∙ OMIM:617815 ∙ HGNC:30347 ∙ Uniprot:Q9NVU0 ∙ 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 POLR3E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR3E 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			55	4	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	5	1

Variants in POLR3E

This is a list of pathogenic ClinVar variants found in the POLR3E region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22305171-G-T		not specified	Uncertain significance (May 05, 2023)
16-22308178-G-C			Uncertain significance (Jun 10, 2022)
16-22308190-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-22308197-C-T		not specified	Uncertain significance (Mar 31, 2022)
16-22308965-A-G		not specified	Uncertain significance (Oct 27, 2023)
16-22308971-G-A		not specified	Uncertain significance (Oct 11, 2024)
16-22308975-C-A		not specified	Uncertain significance (Aug 28, 2021)
16-22308992-C-T		not specified	Uncertain significance (Aug 21, 2023)
16-22309025-C-T		not specified	Uncertain significance (Apr 26, 2024)
16-22309469-C-T		not specified	Uncertain significance (Dec 31, 2023)
16-22309492-G-A		not specified	Uncertain significance (Jan 02, 2024)
16-22309505-G-A		not specified	Uncertain significance (Oct 22, 2021)
16-22313625-C-T		not specified	Uncertain significance (May 24, 2023)
16-22313631-C-G		not specified	Uncertain significance (Dec 04, 2024)
16-22313650-T-C		not specified	Uncertain significance (May 30, 2022)
16-22313704-G-A		not specified	Uncertain significance (Sep 27, 2022)
16-22313723-C-T			Likely benign (Apr 01, 2022)
16-22315105-C-T		not specified	Uncertain significance (Oct 26, 2024)
16-22315123-G-A		not specified	Uncertain significance (Jun 25, 2024)
16-22315138-A-G		not specified	Uncertain significance (Oct 20, 2023)
16-22315185-C-T		not specified	Uncertain significance (Apr 24, 2024)
16-22316623-G-A		not specified	Uncertain significance (Jul 31, 2024)
16-22316652-G-A		not specified	Uncertain significance (Apr 08, 2024)
16-22316667-G-A		not specified	Uncertain significance (May 04, 2022)
16-22317029-G-A		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR3E	protein_coding	protein_coding	ENST00000299853	20	37695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0132	0.987	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	364	457	0.797	0.0000304	4633
Missense in Polyphen		62	98.89	0.62696		985
Synonymous	-1.84	230	197	1.17	0.0000143	1364
Loss of Function	4.37	12	42.9	0.280	0.00000217	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000626	0.0000626
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000232	0.000231
European (Non-Finnish)	0.0000726	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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. Essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters. 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 (By similarity). {ECO:0000250, ECO:0000269|PubMed:19609254, ECO:0000269|PubMed:19631370}.
• 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;Eukaryotic Transcription Initiation;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: 0.145

Intolerance Scores

• loftool: 0.544
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.32

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.602
• ghis: 0.596

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr3e

Gene ontology

• Biological process: transcription by RNA polymerase III;innate immune response;defense response to virus
• Cellular component: nucleus;nucleoplasm;RNA polymerase III complex;cytosol
• Molecular function: RNA polymerase III activity