POLR3D

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

Basic information

Region (hg38): 8:22245133-22254601

Previous symbols: [ "BN51T" ]

Links

ENSG00000168495 ∙ NCBI:661 ∙ OMIM:187280 ∙ HGNC:1080 ∙ Uniprot:P05423 ∙ 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 POLR3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR3D 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						0
missense			42			42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	0	0

Variants in POLR3D

This is a list of pathogenic ClinVar variants found in the POLR3D region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22245487-C-G		not specified	Uncertain significance (May 04, 2022)
8-22245499-G-A		not specified	Uncertain significance (Dec 21, 2022)
8-22245499-G-T		not specified	Uncertain significance (Jan 16, 2024)
8-22245511-C-T		not specified	Uncertain significance (Oct 13, 2023)
8-22245516-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-22245519-C-G		not specified	Uncertain significance (Oct 12, 2024)
8-22245537-C-T		not specified	Uncertain significance (Feb 21, 2024)
8-22245549-C-T		not specified	Uncertain significance (May 20, 2024)
8-22245559-C-G		not specified	Uncertain significance (May 09, 2023)
8-22245588-G-C		not specified	Uncertain significance (Dec 06, 2024)
8-22247246-G-T		not specified	Uncertain significance (Nov 07, 2023)
8-22247868-A-G		not specified	Uncertain significance (Aug 04, 2023)
8-22247910-G-A		not specified	Uncertain significance (Aug 15, 2023)
8-22247916-G-A		not specified	Uncertain significance (Jan 16, 2024)
8-22247919-A-C		not specified	Uncertain significance (Apr 12, 2023)
8-22247937-G-A		not specified	Uncertain significance (Nov 25, 2024)
8-22248158-C-G		not specified	Uncertain significance (Oct 19, 2024)
8-22248165-A-G		not specified	Uncertain significance (May 17, 2023)
8-22248171-G-A		not specified	Uncertain significance (Sep 08, 2024)
8-22248258-C-T		not specified	Uncertain significance (Jul 20, 2021)
8-22248267-G-A		not specified	Uncertain significance (Sep 17, 2021)
8-22248276-G-A		not specified	Uncertain significance (Oct 05, 2023)
8-22248487-G-A		not specified	Uncertain significance (May 24, 2023)
8-22248556-C-T		not specified	Uncertain significance (Mar 01, 2024)
8-22248644-T-G		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR3D	protein_coding	protein_coding	ENST00000397802	8	9497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.83e-11	0.177	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.358	195	210	0.930	0.0000115	2568
Missense in Polyphen		40	54.416	0.73507		668
Synonymous	-0.805	90	80.8	1.11	0.00000463	814
Loss of Function	0.684	18	21.4	0.841	0.00000155	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000652	0.000652
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000272	0.000272
South Asian	0.000425	0.000425
Other	0.000164	0.000163

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. 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;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.381
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.454
• hipred: Y
• hipred_score: 0.602
• ghis: 0.575

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr3d

Gene ontology

• Biological process: 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: nuclear chromatin;nucleoplasm;RNA polymerase III complex;cytosol;nuclear speck
• Molecular function: RNA polymerase III activity;DNA binding;chromatin binding