POLR3GL

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

Basic information

Region (hg38): 1:145964690-145978848

Links

ENSG00000121851 ∙ NCBI:84265 ∙ OMIM:617457 ∙ HGNC:28466 ∙ Uniprot:Q9BT43 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature, oligodontia, dysmorphic facies, and motor delay	AR	General	Among other findings, the condition may include potentially occult cardiovascular anomalies, and awareness may enable surveillance, early diagnosis, and management	Cardiovascular; Craniofacial; Dental; Musculoskeletal; Neurologic	31089205; 31695177

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POLR3GL gene.

• POLR3GL-related disorder (2 variants)
• Short stature, oligodontia, dysmorphic facies, and motor delay (2 variants)
• Oligodontia;Abnormal facial shape;Short stature;Hyperostosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR3GL 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			19			19
nonsense	1					1
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	2	0	20	2	0

Highest pathogenic variant AF is 0.0000131

Variants in POLR3GL

This is a list of pathogenic ClinVar variants found in the POLR3GL region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145974824-G-A		Abnormal facial shape;Short stature;Hyperostosis;Oligodontia • Short stature, oligodontia, dysmorphic facies, and motor delay • POLR3GL-related disorder	Pathogenic (Aug 21, 2023)
1-145974867-T-C		not specified	Uncertain significance (Nov 15, 2023)
1-145974891-G-A		not specified	Uncertain significance (Nov 13, 2023)
1-145974900-G-A		not specified	Uncertain significance (May 31, 2023)
1-145975383-G-C		not specified	Uncertain significance (Oct 29, 2024)
1-145975415-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-145975416-G-A		not specified	Uncertain significance (Jul 14, 2022)
1-145977093-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-145977109-T-C			Likely benign (Jan 01, 2023)
1-145977137-A-C		not specified	Uncertain significance (Feb 16, 2023)
1-145977137-A-G		not specified	Uncertain significance (Oct 16, 2024)
1-145977482-G-A		Short stature;Oligodontia;Abnormal facial shape;Hyperostosis • Short stature, oligodontia, dysmorphic facies, and motor delay	Pathogenic/Likely pathogenic (Mar 17, 2021)
1-145977489-G-A		not specified	Uncertain significance (Oct 16, 2024)
1-145977491-C-T		not specified	Uncertain significance (Jun 01, 2023)
1-145977501-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-145977515-C-T		Short stature, oligodontia, dysmorphic facies, and motor delay • POLR3GL-related disorder	Pathogenic (Aug 21, 2023)
1-145977522-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-145977824-T-A		not specified	Uncertain significance (Jun 25, 2024)
1-145977828-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-145977998-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-145978026-A-G		not specified	Uncertain significance (Apr 25, 2023)
1-145978030-G-C		not specified	Uncertain significance (Apr 22, 2022)
1-145978046-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-145978075-T-C			Likely benign (Oct 01, 2023)
1-145978392-A-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR3GL	protein_coding	protein_coding	ENST00000369314	7	14153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000234	0.756	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.339	112	123	0.914	0.00000694	1411
Missense in Polyphen		40	45.771	0.87391		515
Synonymous	0.536	39	43.5	0.897	0.00000234	407
Loss of Function	1.13	9	13.5	0.668	6.79e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000327	0.000326

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. {ECO:0000269|PubMed:20154270}.
• 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: 0.115

Intolerance Scores

• loftool: 0.519
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.429
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr3gl

Gene ontology

• Biological process: transcription by RNA polymerase III
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;RNA polymerase III complex;cytosol
• Molecular function: DNA-directed 5'-3' RNA polymerase activity;protein binding