POLR3GL

protein-coding

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

Gene summary

Predicted to enable chromatin binding activity. Involved in transcription by RNA polymerase III. Located in nucleus. Part of RNA polymerase III complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_032305.3

Inheritance

ClinVar variants

P:3U:37B:2

Top phenotype

Short stature, oligodontia, dysmorphic facies, and motor delay

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr1:145,964,690-145,978,848

External References & Databases

Ensembl (ENSG00000121851)

Transcript & Mutation Effects

hg38 • Region Span ~14.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

short stature, oligodontia, dysmorphic facies, and motor delayMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030992

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Short stature, oligodontia, dysmorphic facies, and motor delayAR

Manifestation: Cardiovascular; Craniofacial; Dental; Musculoskeletal; Neurologic

Intervention: General

Rationale: Among other findings, the condition may include potentially occult cardiovascular anomalies, and awareness may enable surveillance, early diagnosis, and management

Refs: 31089205; 31695177

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to POLR3GL variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 33

Short stature, oligodontia, dysmorphic facies, and motor delayTotal: 3

not providedTotal: 2

Short statureTotal: 2

Abnormal facial shapeTotal: 2

POLR3GL-related disorderTotal: 2

HyperostosisTotal: 2

OligodontiaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032305.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			33 clinvar			33
nonsense	1 clinvar					1
start loss			1 clinvar			1
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar	1 clinvar			3
Total	2	1	37	2	0	42

Highest pathogenic variant AF is 0.000037202128

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032305.3	RefSeq	NP_115681.1	7	MANE Select
ENST00000369314.2	Ensembl	ENSP00000358320.1	7	MANE Select
NM_001330685.2	RefSeq	NP_001317614.1	6	Standard
ENST00000369313.7	Ensembl	ENSP00000358319.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

transcription by RNA polymerase III

Molecular Function

DNA-directed 5'-3' RNA polymerase activity
protein binding

Cellular Component

nuclear chromatin
nucleus
nucleoplasm
RNA polymerase III complex
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369314
Coding exons: 7
Length: 14153
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.339	112	123	0.914	0.00000694	1411
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.519
RVIS EVS: -0.1
RVIS percentile EVS: 46.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.120

Gene Damage Prediction

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