POLR3H

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

Basic information

Region (hg38): 22:41525798-41544606

Links

ENSG00000100413 ∙ NCBI:171568 ∙ OMIM:619801 ∙ HGNC:30349 ∙ Uniprot:Q9Y535 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 46 XX gonadal dysgenesis (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POLR3H gene.

• not provided (170 variants)
• Inborn genetic diseases (16 variants)
• not specified (11 variants)
• Infantile cerebellar-retinal degeneration (11 variants)
• Optic atrophy 9 (6 variants)
• OPTIC ATROPHY 9, AUTOSOMAL RECESSIVE (2 variants)
• Infantile cerebellar-retinal degeneration;Optic atrophy 9 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR3H 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding	10	4	71	80	8	173
Total	10	4	83	80	8

Highest pathogenic variant AF is 0.00000657

Variants in POLR3H

This is a list of pathogenic ClinVar variants found in the POLR3H region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41526182-GCTGC-G			Benign (Jan 06, 2020)
22-41526227-G-T			Likely benign (Aug 30, 2018)
22-41526241-CCT-C			Likely benign (Jul 16, 2023)
22-41526242-C-G			Likely benign (Aug 09, 2022)
22-41526241-C-CCTCTCTA			Likely benign (Jan 07, 2021)
22-41526244-C-T			Likely benign (Sep 06, 2023)
22-41526246-C-T			Likely benign (Aug 19, 2022)
22-41526253-C-A			Likely benign (Aug 10, 2022)
22-41526262-G-A			Uncertain significance (Jun 28, 2022)
22-41526270-G-A		not specified	Likely benign (Nov 02, 2023)
22-41526275-G-A			Uncertain significance (Mar 26, 2022)
22-41526276-T-A		Infantile cerebellar-retinal degeneration	Pathogenic (Aug 01, 2021)
22-41526276-T-C			Likely benign (Dec 25, 2023)
22-41526287-A-G		Infantile cerebellar-retinal degeneration	Pathogenic (Sep 16, 2020)
22-41526289-A-G			Uncertain significance (Jul 25, 2022)
22-41526302-G-A			Conflicting classifications of pathogenicity (Aug 09, 2022)
22-41526316-T-TTCCGTGGGCACTTGGATAACATCTCCAACAACCTGCTCATTGGTGCCATCAACATTGAAAACGGCAAGGCCAAC		Optic atrophy 9	Likely pathogenic (Jun 23, 2022)
22-41526319-C-T		Infantile cerebellar-retinal degeneration	Conflicting classifications of pathogenicity (Jan 10, 2023)
22-41526320-G-A			Uncertain significance (Aug 04, 2023)
22-41526330-G-A			Likely benign (Nov 30, 2022)
22-41526331-GAT-C		Optic atrophy 9	Likely pathogenic (Jan 09, 2024)
22-41526331-GA-G			Pathogenic (Aug 15, 2022)
22-41526333-T-TA			Pathogenic (Aug 31, 2022)
22-41526336-C-T			Likely benign (Oct 05, 2022)
22-41526338-TCTC-T			Uncertain significance (Oct 27, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR3H	protein_coding	protein_coding	ENST00000355209	6	18803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00599	0.913	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.136	123	127	0.966	0.00000742	1340
Missense in Polyphen		47	41.695	1.1272		472
Synonymous	-1.93	71	53.1	1.34	0.00000357	387
Loss of Function	1.50	5	10.2	0.492	4.31e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
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. 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: 0.122

Intolerance Scores

• loftool: 0.122
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.813
• ghis: 0.624

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr3h

Zebrafish Information Network

• Gene name: polr3h
• Affected structure: hematopoietic multipotent progenitor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;transcription by RNA polymerase III;transcription initiation from RNA polymerase III promoter;innate immune response;defense response to virus
• Cellular component: nucleoplasm;RNA polymerase III complex;centrosome;cytosol;intracellular membrane-bounded organelle
• Molecular function: RNA polymerase III activity;DNA binding;DNA-directed 5'-3' RNA polymerase activity