POLR3A
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Also known as RPC1RPC155hRPC155C160
Summary
POLR3A (RNA polymerase III subunit A, HGNC:30074) is a protein-coding gene on chromosome 10q22.3, encoding DNA-directed RNA polymerase III subunit RPC1 (O14802). Catalytic core component of RNA polymerase III (Pol III), a DNA-dependent RNA polymerase which synthesizes small non-coding RNAs using the four ribonucleoside triphosphates as substrates. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).
The protein encoded by this gene is the catalytic component of RNA polymerase III, which synthesizes small RNAs. The encoded protein also acts as a sensor to detect foreign DNA and trigger an innate immune response.
Source: NCBI Gene 11128 — RefSeq curated summary.
At a glance
- Gene–disease (curated): POLR3A-related disorder (Definitive, ClinGen) — +7 more curated relationships
- GWAS associations: 3
- Clinical variants (ClinVar): 1,241 total — 51 pathogenic, 50 likely-pathogenic
- Phenotypes (HPO): 224
- Druggable target: yes
- Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
- MANE Select transcript:
NM_007055
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:30074 |
| Approved symbol | POLR3A |
| Name | RNA polymerase III subunit A |
| Location | 10q22.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | RPC1, RPC155, hRPC155, C160 |
| Ensembl gene | ENSG00000148606 |
| Ensembl biotype | protein_coding |
| OMIM | 614258 |
| Entrez | 11128 |
Gene structure
Transcript identifiers
Ensembl transcripts: 24 — 12 retained_intron, 6 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined
ENST00000372371, ENST00000472014, ENST00000473588, ENST00000484760, ENST00000698724, ENST00000698725, ENST00000698726, ENST00000698727, ENST00000698728, ENST00000698729, ENST00000698730, ENST00000698731, ENST00000698732, ENST00000698733, ENST00000698734, ENST00000698735, ENST00000698736, ENST00000698737, ENST00000698738, ENST00000698739, ENST00000865317, ENST00000865318, ENST00000912219, ENST00000912220
RefSeq mRNA: 1 — MANE Select: NM_007055
NM_007055
CCDS: CCDS7354
Canonical transcript exons
ENST00000372371 — 31 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000933817 | 78019162 | 78019265 |
| ENSE00000986168 | 78025622 | 78025759 |
| ENSE00000986169 | 78024971 | 78025142 |
| ENSE00000986171 | 78022145 | 78022384 |
| ENSE00000986172 | 78021860 | 78022022 |
| ENSE00000986173 | 78021546 | 78021682 |
| ENSE00000986178 | 78009537 | 78009675 |
| ENSE00000986182 | 78000976 | 78001094 |
| ENSE00000986183 | 77999981 | 78000118 |
| ENSE00000986187 | 77985903 | 77985985 |
| ENSE00001092878 | 78026094 | 78026229 |
| ENSE00001092882 | 77985170 | 77985340 |
| ENSE00001092891 | 78024549 | 78024703 |
| ENSE00001457628 | 77975149 | 77977626 |
| ENSE00001457649 | 78029364 | 78029515 |
| ENSE00003290684 | 78010471 | 78010540 |
| ENSE00003330153 | 78013650 | 78013790 |
| ENSE00003416948 | 78009864 | 78009991 |
| ENSE00003475872 | 78017575 | 78017716 |
| ENSE00003508805 | 78007702 | 78007866 |
| ENSE00003628599 | 78002197 | 78002308 |
| ENSE00003676833 | 78004716 | 78004888 |
| ENSE00003974560 | 77984205 | 77984298 |
| ENSE00003974566 | 77983920 | 77984012 |
| ENSE00003974585 | 77981428 | 77981559 |
| ENSE00003974586 | 77980141 | 77980273 |
| ENSE00003974587 | 77993197 | 77993367 |
| ENSE00003974589 | 77982154 | 77982318 |
| ENSE00003974597 | 77991054 | 77991167 |
| ENSE00003974600 | 77982653 | 77982817 |
| ENSE00003974607 | 77986073 | 77986159 |
Expression profiles
Bgee: expression breadth ubiquitous, 242 present calls, max score 92.39.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.4642 / max 153.7318, expressed in 1804 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 110209 | 15.7384 | 1792 |
| 110210 | 2.7257 | 1330 |
Top tissues by expression
251 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| buccal mucosa cell | CL:0002336 | 92.39 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 90.05 | gold quality |
| secondary oocyte | CL:0000655 | 89.75 | gold quality |
| tibialis anterior | UBERON:0001385 | 89.02 | silver quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 88.03 | gold quality |
| endothelial cell | CL:0000115 | 87.70 | gold quality |
| upper arm skin | UBERON:0004263 | 87.29 | silver quality |
| kidney epithelium | UBERON:0004819 | 86.94 | silver quality |
| cortical plate | UBERON:0005343 | 86.83 | gold quality |
| oocyte | CL:0000023 | 86.02 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 85.73 | gold quality |
| parietal lobe | UBERON:0001872 | 85.27 | gold quality |
| postcentral gyrus | UBERON:0002581 | 85.27 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 84.93 | gold quality |
| cerebellar vermis | UBERON:0004720 | 84.71 | gold quality |
| entorhinal cortex | UBERON:0002728 | 84.29 | gold quality |
| deltoid | UBERON:0001476 | 84.24 | silver quality |
| ganglionic eminence | UBERON:0004023 | 83.57 | gold quality |
| stromal cell of endometrium | CL:0002255 | 83.50 | gold quality |
| primary visual cortex | UBERON:0002436 | 83.47 | gold quality |
| occipital lobe | UBERON:0002021 | 83.41 | gold quality |
| nipple | UBERON:0002030 | 83.30 | gold quality |
| gastrocnemius | UBERON:0001388 | 82.86 | gold quality |
| islet of Langerhans | UBERON:0000006 | 82.76 | gold quality |
| muscle of leg | UBERON:0001383 | 82.60 | gold quality |
| prefrontal cortex | UBERON:0000451 | 82.55 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 82.52 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 82.49 | gold quality |
| frontal cortex | UBERON:0001870 | 82.41 | gold quality |
| quadriceps femoris | UBERON:0001377 | 82.25 | silver quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 6.11 |
| E-MTAB-6386 | no | 516.89 |
| E-GEOD-124858 | no | 222.96 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): E2F1
miRNA regulators (miRDB)
74 targeting POLR3A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-4673 | 100.00 | 66.64 | 1490 |
| HSA-MIR-4500 | 99.99 | 72.72 | 2367 |
| HSA-LET-7A-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7B-5P | 99.98 | 72.31 | 1790 |
| HSA-LET-7C-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7E-5P | 99.98 | 72.29 | 1790 |
| HSA-LET-7F-5P | 99.98 | 72.56 | 1784 |
| HSA-LET-7G-5P | 99.98 | 72.37 | 1784 |
| HSA-LET-7I-5P | 99.98 | 72.37 | 1788 |
| HSA-MIR-98-5P | 99.98 | 72.33 | 1787 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-MIR-4645-5P | 99.98 | 65.81 | 1284 |
| HSA-MIR-4650-5P | 99.98 | 64.69 | 999 |
| HSA-MIR-5688 | 99.96 | 73.23 | 4504 |
| HSA-MIR-495-3P | 99.96 | 72.81 | 4197 |
| HSA-MIR-146A-5P | 99.96 | 68.93 | 988 |
| HSA-MIR-146B-5P | 99.96 | 69.13 | 977 |
| HSA-MIR-590-3P | 99.96 | 74.34 | 6478 |
| HSA-MIR-570-3P | 99.96 | 72.41 | 4910 |
| HSA-LET-7D-5P | 99.96 | 71.76 | 1632 |
| HSA-MIR-4458 | 99.96 | 71.64 | 1650 |
| HSA-MIR-548AJ-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-548X-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-1236-3P | 99.94 | 68.04 | 1695 |
| HSA-MIR-7153-5P | 99.94 | 68.89 | 1006 |
| HSA-MIR-7-1-3P | 99.91 | 71.53 | 4384 |
| HSA-MIR-7-2-3P | 99.91 | 71.40 | 4394 |
| HSA-MIR-7162-3P | 99.89 | 68.16 | 1682 |
| HSA-MIR-3151-5P | 99.86 | 63.83 | 1069 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.
Literature-anchored findings (GeneRIF, showing 40)
- Mutations of POLR3A encoding a catalytic subunit of RNA polymerase Pol III cause a recessive hypomyelinating leukodystrophy. (PMID:21855841)
- Mutations in POLR3A and POLR3B encoding RNA Polymerase III subunits cause an autosomal-recessive hypomyelinating leukoencephalopathy (PMID:22036171)
- Studies indicate that aatients with anti-RNAP have an increased risk of malignancy within a 5-year timeframe before or after onset of systemic sclerosis (SSc) skin changes. (PMID:22189167)
- Investigated POLR3A and POLR3B mutations in patients with genetically unexplained hypomyelinating leukodystrophies with features of Pol III-related leukodystrophies. Recessive mutations in POLR3A or POLR3B were uncovered in all 14 patients. (PMID:23355746)
- MRI in patients with POLR3B mutations revealed smaller cerebellar structures, especially vermis, than those in POLR3A mutations. MRI also showed milder hypomyelination in patients with POLR3B mutations than those with POLR3A mutations (PMID:23643445)
- Mutations in POLR3A are associated with a more severe clinical course of 4H leukodystrophy. (PMID:25339210)
- Mutations in POLR3A or POLR3B are rare in patients with unclassified hypomyelination. (PMID:26011300)
- Multicenter retrospective study to collect neuroradiologic, clinical, and molecular data of patients with mutations in POLR3A and POLR3B without the classic MRI phenotype: diffuse hypomyelination is not an obligatory feature of POLR3-related disorders; two distinct patterns, selective involvement of the corticospinal tracts and cerebellar atrophy, are added to the MRI presentation of POLR3-related disorders (PMID:27029625)
- For some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNA pools that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states. (Review) (PMID:27068803)
- Our transcriptome-wide investigations revealed an overall decrease in the levels of Pol III-transcribed tRNAs and an imbalance in the levels of regulatory ncRNAs such as small nuclear and nucleolar RNAs (snRNAs and snoRNAs). (PMID:27506977)
- This is the first individual reported with two truncating POLR3A variants, suggesting that biallelic severe loss of function variants are associated with WRS. Sequencing of POLR3A and perhaps related genes such as POLR3B in additional patients with clinical findings of WRS is needed to prove this gene-disease association. (PMID:27612211)
- RNA polymerase III (RNAPIII) is specialized for transcription of short, abundant nonprotein-coding RNA transcripts. (PMID:27911719)
- the first transgenic mice with a leukodystrophy-causing Polr3a mutation do not recapitulate the childhood-onset hypomyelinating leukodystrophy observed in the majority of human patients with POLR3A mutations. (PMID:28407788)
- Mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia. (PMID:28459997)
- Findings suggest that AP-1 factors are regulators of RNA polymerase III (Pol III)-driven 5S rRNA and U6 snRNA expression with a potential role in cell proliferation. (PMID:28488757)
- monogenic or digenic POLR3A and POLR3C deficiencies confer increased susceptibility to severe VZV disease in otherwise healthy children, providing evidence for an essential role of a DNA sensor in human immunity (PMID:28783042)
- RNA polymerase III (Pol III) transcribes medium-sized non-coding RNAs (collectively termed Pol III genes), and data show that when Pol III genes are hypo-methylated, MYC amplifies their transcription, regardless of its recognition DNA motif. (PMID:28846112)
- Mutations in the coding region of POLR3A cause impaired expression of antiviral cytokines and susceptibility to varicella-zoster virus CNS infection. (PMID:29728610)
- Here, the authors identified multiple RNA regions in Kaposi’s sarcoma-associated herpesvirus as potential virus ligands that bind to RIG-I and stimulate RIG-I-dependent but RNA Pol III-independent IFN-beta signaling. (PMID:29970461)
- RNA polymerase III is a gatekeeper to prevent severe Varicella Zoster virus infections. (Review) (PMID:30115567)
- Biallelic mutations in POLR3A, which encodes for the largest subunit of the DNA-dependent RNA polymerase III, underlie WRS. No isolated functional sites in POLR3A explain the phenotype variability in POLR3A-related disorders. We suggest that specific combinations of compound heterozygous variants must be present to cause the WRS phenotype. (PMID:30323018)
- The association of bi-allelic POLR3A variants with WRS. (PMID:30414627)
- we firmly establish biallelic mutations in POLR3A as the genetic cause of a recognizable, neonatal, Wiedemann-Rautenstrauch-like progeroid syndrome. Thus, we suggest that POLR3A mutations are causal for a portion of under-diagnosed early-onset segmental progeroid syndromes (PMID:30450527)
- Of the 8 previously reported WRS-affected individuals at University of Texas Southwestern, 2 of them had bi-allelic POLR3A variants and 2 others each had de novo variants in FBN1 and CAV1, but the genetic basis for the disorder found in the other 2 remains unclear. At Washington University, all 5 WRS-affected individuals had bi-allelic POLR3A variants. (PMID:30690919)
- findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3-HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease (PMID:30898877)
- Novel mutations of the POLR3A gene caused POLR3-related leukodystrophy in a Chinese family: a case report. (PMID:31438894)
- POLR3A-related spastic ataxia: new mutations and a look into the phenotype. (PMID:31637490)
- POLR3A variants with striatal involvement and extrapyramidal movement disorder. (PMID:31940116)
- Structural basis for RNA polymerase III transcription repression by Maf1 in humans and yeast has been uncovered. (PMID:32066962)
- Runx2 mediates the deregulation of Brf1 and Pol III genes and its abnormal expression predicts the worse prognosis of breast cancer. (PMID:32198086)
- Identification of a deep intronic POLR3A variant causing inclusion of a pseudoexon derived from an Alu element in Pol III-related leukodystrophy. (PMID:32483275)
- Estimating the relative frequency of leukodystrophies and recommendations for carrier screening in the era of next-generation sequencing. (PMID:32573057)
- A novel POLR3A genotype leads to leukodystrophy type-7 in two siblings with unusually late age of onset. (PMID:32600288)
- Endocrine and Growth Abnormalities in 4H Leukodystrophy Caused by Variants in POLR3A, POLR3B, and POLR1C. (PMID:33005949)
- Functional characterization of Polr3a hypomyelinating leukodystrophy mutations in the S. cerevisiae homolog, RPC160. (PMID:33148458)
- Two intronic cis-acting variants in both alleles of the POLR3A gene cause progressive spastic ataxia with hypodontia. (PMID:33491183)
- Wiedemann-Rautenstrauch syndrome in an Indian patient with biallelic pathogenic variants in POLR3A. (PMID:33559318)
- RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination. (PMID:33626331)
- POLR3A variants in hereditary spastic paraparesis and ataxia: clinical, genetic, and neuroradiological findings in a cohort of Italian patients. (PMID:34296356)
- Distinguishing severe phenotypes associated with pathogenic variants in POLR3A. (PMID:34773388)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | polr3a | ENSDARG00000102569 |
| mus_musculus | Polr3a | ENSMUSG00000025280 |
| rattus_norvegicus | Polr3a | ENSRNOG00000010008 |
| drosophila_melanogaster | Polr3A | FBGN0030687 |
| caenorhabditis_elegans | WBGENE00004411 |
Paralogs (2): POLR1A (ENSG00000068654), POLR2A (ENSG00000181222)
Protein
Protein identifiers
DNA-directed RNA polymerase III subunit RPC1 — O14802 (reviewed: O14802)
Alternative names: DNA-directed RNA polymerase III largest subunit, DNA-directed RNA polymerase III subunit A, RNA polymerase III 155 kDa subunit, RNA polymerase III subunit C160
All UniProt accessions (6): O14802, A0A8V8TM36, A0A8V8TM70, A0A8V8TNL6, A0A8V8TNX3, R4GMX2
UniProt curated annotations — full annotation on UniProt →
Function. Catalytic core component of RNA polymerase III (Pol III), a DNA-dependent RNA polymerase which synthesizes small non-coding RNAs using the four ribonucleoside triphosphates as substrates. Synthesizes 5S rRNA, snRNAs, tRNAs and miRNAs from at least 500 distinct genomic loci. Pol III-mediated transcription cycle proceeds through transcription initiation, transcription elongation and transcription termination stages. During transcription initiation, Pol III is recruited to DNA promoters type I, II or III with the help of general transcription factors and other specific initiation factors. Once the polymerase has escaped from the promoter it enters the elongation phase during which RNA is actively polymerized, based on complementarity with the template DNA strand. Transcription termination involves the release of the RNA transcript and polymerase from the DNA. Forms Pol III active center together with the second largest subunit POLR3B/RPC2. Appends one nucleotide at a time to the 3’ end of the nascent RNA, with POLR3A/RPC1 contributing a Mg(2+)-coordinating DxDGD motif, and POLR3B/RPC2 participating in the coordination of a second Mg(2+) ion and providing lysine residues believed to facilitate Watson-Crick base pairing between the incoming nucleotide and template base. Typically, Mg(2+) ions direct a 5’ nucleoside triphosphate to form a phosphodiester bond with the 3’ hydroxyl of the preceding nucleotide of the nascent RNA, with the elimination of pyrophosphate. Pol III plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as a 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.
Subunit / interactions. Component of the RNA polymerase III (Pol III) (Pol III) complex consisting of 17 subunits: a ten-subunit catalytic core composed of POLR3A/RPC1, POLR3B/RPC2, POLR1C/RPAC1, POLR1D/RPAC2, POLR3K/RPC10, POLR2E/RPABC1, POLR2F/RPABC2, POLR2H/RPABC3, POLR2K/RPABC4 and POLR2L/RPABC5; a mobile stalk composed of two subunits POLR3H/RPC8 and CRCP/RPC9, protruding from the core and functioning primarily in transcription initiation; and additional subunits homologous to general transcription factors of the RNA polymerase II machinery, POLR3C/RPC3-POLR3F/RPC6-POLR3G/RPC7 heterotrimer required for transcription initiation and POLR3D/RPC4-POLR3E/RPC5 heterodimer involved in both transcription initiation and termination. Pol III exists as two alternative complexes defined by the mutually exclusive incorporation of subunit POLR3G/RPC7alpha or POLR3GL/RPC7beta. The presence of POLR3G/RPC7alpha or POLR3GL/RPC7beta differentially modulates the transcription potential of Pol III, with POLR3G/RPC7alpha specifically associated with transcription of snaR-A non-coding RNAs. As part of the RNA polymerase III complex, interacts with PKP2.
Subcellular location. Nucleus. Cytoplasm. Cytosol.
Tissue specificity. Expressed in the brain, in the cortex and the white matter (at protein level).
Disease relevance. Leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism (HLD7) [MIM:607694] An autosomal recessive neurodegenerative disorder characterized by childhood onset of progressive motor decline manifest as spasticity, ataxia, tremor, and cerebellar signs, as well as mild cognitive regression. Other features may include hypodontia or oligodontia and hypogonadotropic hypogonadism. There is considerable inter- and intrafamilial variability. The disease is caused by variants affecting the gene represented in this entry. Wiedemann-Rautenstrauch syndrome (WDRTS) [MIM:264090] An autosomal recessive, neonatal progeroid disorder characterized by intrauterine growth retardation, failure to thrive, short stature, hypotonia, variable mental impairment, and a progeroid appearance. Clinical features include apparent macrocephaly, sparse hair, prominent scalp veins, entropion, greatly widened anterior fontanelles, malar hypoplasia, and generalized lipoatrophy. Death usually occurs in early childhood but survival to third decade has been reported. The disease is caused by variants affecting the gene represented in this entry.
Cofactor. Two Mg(2+) ions are coordinated by both the catalytic residues and the nucleic acid substrate to enhance substrate recognition and catalytic efficiency.
Similarity. Belongs to the RNA polymerase beta’ chain family.
RefSeq proteins (1): NP_008986* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000722 | RNA_pol_asu | Domain |
| IPR006592 | RNA_pol_N | Domain |
| IPR007066 | RNA_pol_Rpb1_3 | Domain |
| IPR007080 | RNA_pol_Rpb1_1 | Domain |
| IPR007081 | RNA_pol_Rpb1_5 | Domain |
| IPR007083 | RNA_pol_Rpb1_4 | Domain |
| IPR015700 | RPC1 | Family |
| IPR035697 | RNAP_III_RPC1_N | Domain |
| IPR035698 | RNAP_III_Rpc1_C | Domain |
| IPR038120 | Rpb1_funnel_sf | Homologous_superfamily |
| IPR042102 | RNA_pol_Rpb1_3_sf | Homologous_superfamily |
| IPR044893 | RNA_pol_Rpb1_clamp_domain | Homologous_superfamily |
Pfam: PF00623, PF04983, PF04997, PF04998, PF05000
Catalyzed reactions (Rhea), 1 shown:
- RNA(n) + a ribonucleoside 5’-triphosphate = RNA(n+1) + diphosphate (RHEA:21248)
UniProt features (210 total): helix 66, strand 63, sequence variant 27, binding site 25, turn 20, sequence conflict 5, region of interest 2, chain 1, modified residue 1
Structure
Experimental structures (PDB)
29 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 7AE1 | ELECTRON MICROSCOPY | 2.8 |
| 9K39 | ELECTRON MICROSCOPY | 2.8 |
| 7D58 | ELECTRON MICROSCOPY | 2.9 |
| 9K36 | ELECTRON MICROSCOPY | 2.9 |
| 9K2G | ELECTRON MICROSCOPY | 3 |
| 9K3U | ELECTRON MICROSCOPY | 3 |
| 7AE3 | ELECTRON MICROSCOPY | 3.1 |
| 7D59 | ELECTRON MICROSCOPY | 3.1 |
| 9K38 | ELECTRON MICROSCOPY | 3.1 |
| 9FSO | ELECTRON MICROSCOPY | 3.28 |
| 7A6H | ELECTRON MICROSCOPY | 3.3 |
| 9LXN | ELECTRON MICROSCOPY | 3.3 |
| 7DU2 | ELECTRON MICROSCOPY | 3.35 |
| 9FSP | ELECTRON MICROSCOPY | 3.39 |
| 7AEA | ELECTRON MICROSCOPY | 3.4 |
| 8IUH | ELECTRON MICROSCOPY | 3.4 |
| 7DN3 | ELECTRON MICROSCOPY | 3.5 |
| 9K3V | ELECTRON MICROSCOPY | 3.5 |
| 9LKT | ELECTRON MICROSCOPY | 3.5 |
| 9FSQ | ELECTRON MICROSCOPY | 3.51 |
| 7FJI | ELECTRON MICROSCOPY | 3.6 |
| 7FJJ | ELECTRON MICROSCOPY | 3.6 |
| 9LXO | ELECTRON MICROSCOPY | 3.6 |
| 9FSR | ELECTRON MICROSCOPY | 3.76 |
| 8ITY | ELECTRON MICROSCOPY | 3.9 |
| 7AST | ELECTRON MICROSCOPY | 4 |
| 8IUE | ELECTRON MICROSCOPY | 4.1 |
| 9FSS | ELECTRON MICROSCOPY | 4.14 |
| 9K3B | ELECTRON MICROSCOPY | 4.8 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O14802-F1 | 88.40 | 0.57 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (25): 156; 159; 167; 326; 348; 353; 360; 366; 464; 499; 499; 501 …
Post-translational modifications (1): 445
Function
Pathways and Gene Ontology
Reactome pathways
12 pathways
| ID | Pathway |
|---|---|
| R-HSA-1834949 | Cytosolic sensors of pathogen-associated DNA |
| R-HSA-73780 | RNA Polymerase III Chain Elongation |
| R-HSA-73980 | RNA Polymerase III Transcription Termination |
| R-HSA-749476 | RNA Polymerase III Abortive And Retractive Initiation |
| R-HSA-76061 | RNA Polymerase III Transcription Initiation From Type 1 Promoter |
| R-HSA-76066 | RNA Polymerase III Transcription Initiation From Type 2 Promoter |
| R-HSA-76071 | RNA Polymerase III Transcription Initiation From Type 3 Promoter |
| R-HSA-168249 | Innate Immune System |
| R-HSA-168256 | Immune System |
| R-HSA-74158 | RNA Polymerase III Transcription |
| R-HSA-74160 | Gene expression (Transcription) |
| R-HSA-76046 | RNA Polymerase III Transcription Initiation |
MSigDB gene sets: 599 (showing top):
REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER, REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_TERMINATION, REACTOME_INNATE_IMMUNE_SYSTEM, REACTOME_RNA_POLYMERASE_III_CHAIN_ELONGATION, GOBP_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION, GOBP_POSITIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY, MARTINEZ_RB1_TARGETS_UP, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_POSITIVE_REGULATION_OF_INTERFERON_BETA_PRODUCTION
GO Biological Process (7): DNA-templated transcription (GO:0006351), positive regulation of interferon-beta production (GO:0032728), tRNA transcription by RNA polymerase III (GO:0042797), innate immune response (GO:0045087), defense response to virus (GO:0051607), immune system process (GO:0002376), positive regulation of gene expression (GO:0010628)
GO Molecular Function (11): magnesium ion binding (GO:0000287), DNA binding (GO:0003677), chromatin binding (GO:0003682), DNA-directed RNA polymerase activity (GO:0003899), zinc ion binding (GO:0008270), DNA/RNA hybrid binding (GO:0071667), protein binding (GO:0005515), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779), 5’-3’ RNA polymerase activity (GO:0034062), metal ion binding (GO:0046872)
GO Cellular Component (8): nucleus (GO:0005634), nucleoplasm (GO:0005654), RNA polymerase III complex (GO:0005666), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), DNA-directed RNA polymerase complex (GO:0000428), nuclear lumen (GO:0031981)
Reactome top-level categories
Rollup of top-5 pathways:
| Category | Pathways |
|---|---|
| RNA Polymerase III Transcription | 4 |
| RNA Polymerase III Transcription Initiation | 3 |
| Innate Immune System | 1 |
| Immune System | 1 |
| Gene expression (Transcription) | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 4 |
| gene expression | 2 |
| RNA biosynthetic process | 2 |
| nucleic acid binding | 2 |
| binding | 2 |
| positive regulation of type I interferon production | 1 |
| interferon-beta production | 1 |
| regulation of interferon-beta production | 1 |
| transcription by RNA polymerase III | 1 |
| tRNA transcription | 1 |
| immune response | 1 |
| defense response to symbiont | 1 |
| defense response | 1 |
| response to virus | 1 |
| biological_process | 1 |
| regulation of gene expression | 1 |
| positive regulation of macromolecule biosynthetic process | 1 |
| metal ion binding | 1 |
| 5’-3’ RNA polymerase activity | 1 |
| transition metal ion binding | 1 |
| catalytic activity | 1 |
| transferase activity, transferring phosphorus-containing groups | 1 |
| RNA polymerase activity | 1 |
| cation binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| nuclear lumen | 1 |
| DNA-directed RNA polymerase complex | 1 |
| nuclear protein-containing complex | 1 |
| intracellular anatomical structure | 1 |
| cytoplasm | 1 |
| RNA polymerase complex | 1 |
| nucleus | 1 |
| intracellular organelle lumen | 1 |
Protein interactions and networks
STRING
4398 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| POLR3A | POLR3B | Q9NW08 | 976 |
| POLR3A | POLR1D | P0DPB6 | 925 |
| POLR3A | MAF1 | Q9H063 | 906 |
| POLR3A | BDP1 | A6H8Y1 | 902 |
| POLR3A | POLR3K | Q9Y2Y1 | 866 |
| POLR3A | POLR3C | Q9BUI4 | 862 |
| POLR3A | POLR3F | Q9H1D9 | 846 |
| POLR3A | POLR3G | O15318 | 831 |
| POLR3A | POLR3E | Q9NVU0 | 813 |
| POLR3A | POLR3GL | Q9BT43 | 811 |
| POLR3A | POLI | Q9UNA4 | 787 |
| POLR3A | POLR3H | Q9Y535 | 782 |
| POLR3A | POLR3D | P05423 | 762 |
| POLR3A | POLR2E | P19388 | 719 |
| POLR3A | GTF3C2 | Q8WUA4 | 689 |
IntAct
197 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| POLR2E | POLR3A | psi-mi:“MI:0914”(association) | 0.870 |
| POLR2E | POLR3A | psi-mi:“MI:0915”(physical association) | 0.870 |
| PPP1CC | CCDC85C | psi-mi:“MI:0914”(association) | 0.740 |
| POLR3GL | POLR3A | psi-mi:“MI:0914”(association) | 0.730 |
| POLR2E | MED19 | psi-mi:“MI:0914”(association) | 0.730 |
| POLR3E | POLR3A | psi-mi:“MI:0914”(association) | 0.730 |
| PPP1CA | CCDC85C | psi-mi:“MI:0914”(association) | 0.670 |
| PPP1CA | CCDC85C | psi-mi:“MI:2364”(proximity) | 0.670 |
| PFDN2 | POLR3A | psi-mi:“MI:0914”(association) | 0.670 |
| POLR3A | PFDN2 | psi-mi:“MI:0915”(physical association) | 0.670 |
| PTGES3 | POLR3A | psi-mi:“MI:0915”(physical association) | 0.670 |
| POLR3D | POLR3A | psi-mi:“MI:0914”(association) | 0.640 |
| RUVBL2 | POLR3A | psi-mi:“MI:0914”(association) | 0.640 |
| RUVBL1 | POLR3A | psi-mi:“MI:0914”(association) | 0.640 |
| POLR2L | RCCD1 | psi-mi:“MI:0914”(association) | 0.640 |
| POLR3K | POLR3A | psi-mi:“MI:0914”(association) | 0.640 |
| POLR2F | POLR3A | psi-mi:“MI:0914”(association) | 0.640 |
BioGRID (320): POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), POLR3A (Affinity Capture-MS), CRCP (Co-fractionation), GTF3C3 (Co-fractionation), HDAC1 (Co-fractionation), HDAC2 (Co-fractionation), IPO9 (Co-fractionation), MRPL17 (Co-fractionation)
ESM2 similar proteins: A4IF62, A5CC92, A8EXK9, A8F0P8, A8GMA8, A8GQW5, A8GV25, B0BWB0, B3CV54, F4JXF9, O14802, O55766, O94666, P04050, P04051, P08968, P0C987, P0C988, P0C989, P10964, P15398, P17545, P17546, P28364, P42486, P91875, Q07KK8, Q11HB4, Q196X0, Q1LSX6, Q1RHD1, Q211D9, Q2GFP4, Q2GJ69, Q3YST4, Q4FLL3, Q4UKD5, Q5FFD8, Q5HC04, Q5ZL98
Diamond homologs: A0PXT9, A2RML8, A3CKD4, A4FWF5, A4IF62, A4YCR0, A5CUC6, A5DCV3, A6UV49, A6VGV0, A8AZI2, A8F4G1, A9A9U9, A9BCH4, B0R8D3, B0RB26, B4U738, B6YT17, B8YB54, C0ZVQ7, C1AYV8, C3MRK4, C3MYA0, C3MZM9, C3N7Q1, C3NFS2, C4KIV9, C5A207, F4JXF9, G3MZY8, O14802, O27126, O28390, O35134, O54889, O93777, O94666, O95602, P04050, P04051
SIGNOR signaling
3 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| POLR3A | up-regulates | Viral_dsRNA | |
| “Cytosolic DNA” | up-regulates | POLR3A | |
| POLR3A | “form complex” | “RNA Polymerase III” | binding |
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 131 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| RNA Polymerase III Chain Elongation | 16 | 120.8× | 8e-31 |
| RNA Polymerase III Transcription Termination | 16 | 94.6× | 3e-28 |
| RNA Polymerase III Transcription Initiation From Type 2 Promoter | 18 | 90.6× | 8e-31 |
| RNA Polymerase III Transcription Initiation From Type 1 Promoter | 18 | 87.4× | 1e-30 |
| RNA Polymerase III Transcription Initiation From Type 3 Promoter | 18 | 87.4× | 1e-30 |
| RNA Polymerase III Transcription Initiation | 18 | 72.0× | 1e-28 |
| RNA Polymerase III Transcription | 18 | 69.9× | 2e-28 |
| RNA Polymerase III Abortive And Retractive Initiation | 18 | 59.7× | 8e-27 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| transcription by RNA polymerase III | 8 | 53.3× | 8e-10 |
| positive regulation of innate immune response | 5 | 22.9× | 5e-04 |
| positive regulation of interferon-beta production | 5 | 17.0× | 1e-03 |
| protein stabilization | 12 | 7.0× | 6e-05 |
| transcription by RNA polymerase II | 10 | 6.1× | 8e-04 |
| defense response to virus | 10 | 6.0× | 8e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
1241 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 51 |
| Likely pathogenic | 50 |
| Uncertain significance | 448 |
| Likely benign | 454 |
| Benign | 81 |
Top pathogenic / likely-pathogenic (30)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1027476 | NM_007055.4(POLR3A):c.3839dup (p.Met1280fs) | Pathogenic |
| 1030186 | NM_007055.4(POLR3A):c.3733C>T (p.Arg1245Ter) | Pathogenic |
| 1034345 | NM_007055.4(POLR3A):c.2323_2329del (p.Asn775fs) | Pathogenic |
| 1184058 | NM_007055.4(POLR3A):c.441dup (p.Asp148Ter) | Pathogenic |
| 1323485 | NM_007055.4(POLR3A):c.1229dup (p.Asn410fs) | Pathogenic |
| 1374074 | NM_007055.4(POLR3A):c.2257_2278dup (p.Arg760fs) | Pathogenic |
| 1427214 | NM_007055.4(POLR3A):c.2658T>A (p.Tyr886Ter) | Pathogenic |
| 1440437 | NM_007055.4(POLR3A):c.112del (p.Ser38fs) | Pathogenic |
| 1449664 | NM_007055.4(POLR3A):c.1608dup (p.Pro537fs) | Pathogenic |
| 1455738 | NM_007055.4(POLR3A):c.2163C>A (p.Tyr721Ter) | Pathogenic |
| 1456249 | NC_000010.10:g.(?79780889)(79784717_?)del | Pathogenic |
| 1460249 | NC_000010.10:g.(?79781284)(79782162_?)del | Pathogenic |
| 1879069 | NM_007055.4(POLR3A):c.646-665_1185+867del | Pathogenic |
| 1903818 | NM_007055.4(POLR3A):c.3951dup (p.Leu1318fs) | Pathogenic |
| 1928113 | NM_007055.4(POLR3A):c.2631_2640del (p.Ser878fs) | Pathogenic |
| 1975923 | NM_007055.4(POLR3A):c.685C>T (p.Arg229Ter) | Pathogenic |
| 2017609 | NM_007055.4(POLR3A):c.2176G>T (p.Glu726Ter) | Pathogenic |
| 2086772 | NM_007055.4(POLR3A):c.2360_2364dup (p.Phe789fs) | Pathogenic |
| 2136897 | NM_007055.4(POLR3A):c.2671C>T (p.Arg891Ter) | Pathogenic |
| 235466 | NM_007055.4(POLR3A):c.2617C>T (p.Arg873Ter) | Pathogenic |
| 2412670 | NM_007055.4(POLR3A):c.3115C>T (p.Gln1039Ter) | Pathogenic |
| 2425680 | NC_000010.10:g.(?79767440)(79770318_?)del | Pathogenic |
| 2425681 | NC_000010.10:g.(?79737218)(79745937_?)del | Pathogenic |
| 2691390 | NC_000010.10:g.(79779024_79781303)_(79782143_79784306)del | Pathogenic |
| 2742457 | NM_007055.4(POLR3A):c.2344del (p.Leu782fs) | Pathogenic |
| 280427 | NM_007055.4(POLR3A):c.491-2A>G | Pathogenic |
| 2842195 | NM_007055.4(POLR3A):c.1325_1326del (p.Gln442fs) | Pathogenic |
| 2996417 | NM_007055.4(POLR3A):c.1738A>T (p.Lys580Ter) | Pathogenic |
| 3018940 | NM_007055.4(POLR3A):c.1784G>A (p.Trp595Ter) | Pathogenic |
| 31147 | NM_007055.4(POLR3A):c.418C>T (p.Arg140Ter) | Pathogenic |
SpliceAI
4107 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 10:77980140:CCA:C | donor_gain | 1.0000 |
| 10:77980140:CCACA:C | donor_gain | 1.0000 |
| 10:77980270:CACC:C | acceptor_gain | 1.0000 |
| 10:77980274:C:CC | acceptor_gain | 1.0000 |
| 10:77980274:CT:C | acceptor_loss | 1.0000 |
| 10:77980280:C:CT | acceptor_gain | 1.0000 |
| 10:77981424:ATACC:A | donor_loss | 1.0000 |
| 10:77981425:TACCT:T | donor_loss | 1.0000 |
| 10:77981426:A:AC | donor_gain | 1.0000 |
| 10:77981427:C:CC | donor_gain | 1.0000 |
| 10:77981556:CCAC:C | acceptor_gain | 1.0000 |
| 10:77981557:CAC:C | acceptor_gain | 1.0000 |
| 10:77981557:CACC:C | acceptor_gain | 1.0000 |
| 10:77981560:C:CC | acceptor_gain | 1.0000 |
| 10:77981561:T:C | acceptor_loss | 1.0000 |
| 10:77981563:C:CT | acceptor_gain | 1.0000 |
| 10:77982315:CCAC:C | acceptor_gain | 1.0000 |
| 10:77982316:CACC:C | acceptor_gain | 1.0000 |
| 10:77982584:AGGTC:A | donor_gain | 1.0000 |
| 10:77982643:T:TA | donor_gain | 1.0000 |
| 10:77983891:T:TA | donor_gain | 1.0000 |
| 10:77983914:ACT:A | donor_loss | 1.0000 |
| 10:77983915:CT:C | donor_loss | 1.0000 |
| 10:77983916:TCACT:T | donor_loss | 1.0000 |
| 10:77983917:CAC:C | donor_loss | 1.0000 |
| 10:77983918:A:AC | donor_gain | 1.0000 |
| 10:77983918:A:C | donor_loss | 1.0000 |
| 10:77983918:ACTT:A | donor_gain | 1.0000 |
| 10:77983919:C:CT | donor_gain | 1.0000 |
| 10:77983919:CTT:C | donor_gain | 1.0000 |
AlphaMissense
9194 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 10:77977584:C:T | G1356E | 1.000 |
| 10:77977585:C:G | G1356R | 1.000 |
| 10:77977585:C:T | G1356R | 1.000 |
| 10:77977602:C:A | G1350V | 1.000 |
| 10:77977602:C:T | G1350E | 1.000 |
| 10:77977603:C:G | G1350R | 1.000 |
| 10:77977603:C:T | G1350R | 1.000 |
| 10:77977608:A:T | I1348N | 1.000 |
| 10:77977620:G:A | S1344F | 1.000 |
| 10:77977620:G:T | S1344Y | 1.000 |
| 10:77977626:C:T | G1342E | 1.000 |
| 10:77980153:C:G | D1338H | 1.000 |
| 10:77980174:C:G | A1331P | 1.000 |
| 10:77980182:A:G | L1328P | 1.000 |
| 10:77980182:A:T | L1328H | 1.000 |
| 10:77980199:C:A | E1322D | 1.000 |
| 10:77980199:C:G | E1322D | 1.000 |
| 10:77980200:T:A | E1322V | 1.000 |
| 10:77980200:T:G | E1322A | 1.000 |
| 10:77980201:C:T | E1322K | 1.000 |
| 10:77980202:A:C | F1321L | 1.000 |
| 10:77980202:A:T | F1321L | 1.000 |
| 10:77980203:A:C | F1321C | 1.000 |
| 10:77980203:A:G | F1321S | 1.000 |
| 10:77980204:A:C | F1321V | 1.000 |
| 10:77980204:A:G | F1321L | 1.000 |
| 10:77980204:A:T | F1321I | 1.000 |
| 10:77980206:G:A | S1320F | 1.000 |
| 10:77980206:G:T | S1320Y | 1.000 |
| 10:77980207:A:G | S1320P | 1.000 |
dbSNP variants (sampled 300 via entrez): RS1000106977 (10:77996935 C>A,T), RS1000132723 (10:77984964 C>T), RS1000139523 (10:77997249 C>T), RS1000185114 (10:77988161 G>A), RS1000216070 (10:77988471 G>A), RS1000264122 (10:78031236 T>G), RS1000320088 (10:77991507 C>T), RS1000349025 (10:78018361 T>C), RS1000399968 (10:77979780 C>T), RS1000412455 (10:77985555 C>G), RS1000493506 (10:77994651 T>C), RS1000649307 (10:77991132 G>A,C), RS1000684935 (10:78007464 A>T), RS1000761454 (10:77979560 G>A,C,T), RS1000774156 (10:77999705 A>G,T)
Disease associations
OMIM: gene MIM:614258 | disease phenotypes: MIM:264090, MIM:607694, MIM:312080, MIM:213002, MIM:614381, MIM:108600, MIM:612233
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| odontoleukodystrophy | Definitive | Autosomal recessive |
| Wiedemann-Rautenstrauch syndrome | Definitive | Autosomal recessive |
| leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism | Strong | Autosomal recessive |
| POLR3A-related disorder | Strong | Autosomal recessive |
| varicella zoster infection | Moderate | Autosomal dominant |
| hypomyelination-cerebellar atrophy-hypoplasia of the corpus callosum syndrome | Supportive | Autosomal recessive |
| tremor-ataxia-central hypomyelination syndrome | Supportive | Autosomal recessive |
| hypomyelination-hypogonadotropic hypogonadism-hypodontia syndrome | Supportive | Autosomal recessive |
ClinGen Gene-Disease Validity (1)
Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.
| Disease | Classification | Inheritance |
|---|---|---|
| POLR3A-related disorder | Definitive | AR |
Mondo (16): Wiedemann-Rautenstrauch syndrome (MONDO:0009910), leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism (MONDO:0011897), leukodystrophy (MONDO:0019046), POLR3A-related disorder (MONDO:0700276), POLR-related leukodystrophy (MONDO:0100605), movement disorder (MONDO:0005395), hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism (MONDO:0013722), spastic ataxia (MONDO:0017845), hereditary ataxia (MONDO:0100309), intellectual disability (MONDO:0001071), hypomyelinating leukodystrophy 4 (MONDO:0012824), odontoleukodystrophy (MONDO:0019177), hypomyelination-cerebellar atrophy-hypoplasia of the corpus callosum syndrome (MONDO:0018655), tremor-ataxia-central hypomyelination syndrome (MONDO:0018656), (MONDO:0019505)
Orphanet (14): Wiedemann-Rautenstrauch syndrome (Orphanet:3455), Hypomyelinating leukodystrophy-ataxia-hypodontia-hypomyelination syndrome (Orphanet:137639), Hypomyelination-cerebellar atrophy-hypoplasia of the corpus callosum syndrome (Orphanet:447893), Tremor-ataxia-central hypomyelination syndrome (Orphanet:447896), Odontoleukodystrophy (Orphanet:77295), Hypomyelination-hypogonadotropic hypogonadism-hypodontia syndrome (Orphanet:88637), Leukodystrophy (Orphanet:68356), 4H leukodystrophy (Orphanet:289494), Hereditary ataxia (Orphanet:183518), Spastic ataxia (Orphanet:316226), Endosteal sclerosis-cerebellar hypoplasia syndrome (Orphanet:85186), Pelizaeus-Merzbacher-like disease (Orphanet:280270), Pelizaeus-Merzbacher-like disease due to HSPD1 mutation (Orphanet:280288), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)
HPO phenotypes
224 total (30 of 224 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000010 | Recurrent urinary tract infections |
| HP:0000028 | Cryptorchidism |
| HP:0000040 | Long penis |
| HP:0000044 | Hypogonadotropic hypogonadism |
| HP:0000047 | Hypospadias |
| HP:0000076 | Vesicoureteral reflux |
| HP:0000126 | Hydronephrosis |
| HP:0000160 | Narrow mouth |
| HP:0000164 | Abnormality of the dentition |
| HP:0000219 | Thin upper lip vermilion |
| HP:0000233 | Thin vermilion border |
| HP:0000238 | Hydrocephalus |
| HP:0000242 | Parietal bossing |
| HP:0000248 | Brachycephaly |
| HP:0000256 | Macrocephaly |
| HP:0000267 | Cranial asymmetry |
| HP:0000272 | Malar flattening |
| HP:0000278 | Retrognathia |
| HP:0000292 | Loss of facial adipose tissue |
| HP:0000307 | Pointed chin |
| HP:0000316 | Hypertelorism |
| HP:0000319 | Smooth philtrum |
| HP:0000322 | Short philtrum |
| HP:0000325 | Triangular face |
| HP:0000336 | Prominent supraorbital ridges |
| HP:0000337 | Broad forehead |
| HP:0000343 | Long philtrum |
| HP:0000347 | Micrognathia |
| HP:0000358 | Posteriorly rotated ears |
GWAS associations
3 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST007694_1 | Executive function (trail making test B) | 7.000000e-06 |
| GCST007856_37 | Colorectal cancer or advanced adenoma | 5.000000e-18 |
| GCST007856_59 | Colorectal cancer or advanced adenoma | 3.000000e-08 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0009332 | executive function measurement |
MeSH disease descriptors (7)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D008607 | Intellectual Disability | C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539 |
| D009069 | Movement Disorders | C10.228.662 |
| C535353 | Cerebellar hypoplasia with endosteal sclerosis (supp.) | |
| C531684 | Hereditary spinal ataxia (supp.) | |
| C567390 | Leukodystrophy, Hypomyelinating, 4 (supp.) | |
| C536423 | Progeroid syndrome, neonatal (supp.) | |
| C564815 | Spastic Ataxia (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: yes
ChEMBL targets (1): CHEMBL4665582 (SINGLE PROTEIN)
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
17 total (human), top 17 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, increases methylation | 2 |
| aristolochic acid I | increases expression | 1 |
| 2,4,6-tribromophenol | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| bisphenol A | decreases methylation | 1 |
| beta-lapachone | decreases expression | 1 |
| arsenite | affects binding, decreases reaction | 1 |
| beta-methylcholine | affects expression | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | decreases expression | 1 |
| Carbamazepine | affects expression | 1 |
| Diclofenac | affects expression | 1 |
| Estradiol | increases expression | 1 |
| Aflatoxin B1 | increases methylation | 1 |
| Okadaic Acid | increases expression | 1 |
| Lactic Acid | decreases expression | 1 |
Cellosaurus cell lines
10 cell lines: 7 induced pluripotent stem cell, 3 embryonic stem cell
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_A5L0 | SEES3-1V human POLR3A, clone1 | Embryonic stem cell | Male |
| CVCL_A5L1 | SEES3-1V human POLR3A, clone2 | Embryonic stem cell | Male |
| CVCL_A5L2 | SEES3-1V human POLR3A, clone3 | Embryonic stem cell | Male |
| CVCL_A8NN | VUi027-A | Induced pluripotent stem cell | Female |
| CVCL_A8NQ | VUi029-A | Induced pluripotent stem cell | Male |
| CVCL_A8NR | VUi030-A | Induced pluripotent stem cell | Female |
| CVCL_D6ID | HIHRSi004-A | Induced pluripotent stem cell | Male |
| CVCL_D6IE | HIHRSi005-A | Induced pluripotent stem cell | Male |
| CVCL_D6IF | HIHRSi006-A | Induced pluripotent stem cell | Male |
| CVCL_D6R4 | CSSi018-A | Induced pluripotent stem cell | Female |
Clinical trials (associated diseases)
306 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT01682109 | PHASE4 | COMPLETED | Palatability Testing of a New Paediatric Formulation of Valacyclovir |
| NCT04403139 | PHASE4 | ACTIVE_NOT_RECRUITING | VZV-specific Tissue Resident Memory T-cells After Shingrix Vaccination |
| NCT01662414 | PHASE4 | COMPLETED | Effect of Undenatured Cysteine-Rich Whey Protein Isolate (HMS 90®) in Patients With Parkinson’s Disease |
| NCT04871464 | PHASE4 | UNKNOWN | Role and Mechanism of Probiotics in Improving Motor Symptoms in Mild to Moderate Parkinson’s Disease |
| NCT06710574 | PHASE4 | RECRUITING | Multimodal Image Technologies Investigate the Role and Mechanism of Probiotics in Improving RBD with Parkinson’s Disease |
| NCT05657860 | PHASE4 | COMPLETED | Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome |
| NCT05744479 | PHASE4 | RECRUITING | Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability |
| NCT06107829 | PHASE4 | WITHDRAWN | Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities |
| NCT06997198 | PHASE4 | NOT_YET_RECRUITING | Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities |
| NCT01838278 | PHASE3 | UNKNOWN | Effectiveness of Vojta Therapy in Motor Development of Preterm Children |
| NCT02270736 | PHASE3 | COMPLETED | Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability |
| NCT00001929 | PHASE2 | COMPLETED | Treatment of Parkinson’s Disease With Eliprodil |
| NCT00331669 | PHASE2 | UNKNOWN | Efficacy and Safety of Deep Brain Stimulation (DBS) of the Pallidal (GPi) in Patients With Tardive Dystonia |
| NCT00406029 | PHASE2 | COMPLETED | Dyskinesia in Parkinson’s Disease (Study P04501) |
| NCT00537017 | PHASE2 | COMPLETED | Follow Up Safety Study of SCH 420814 in Subjects With Parkinson’s Disease (P05175) |
| NCT00693472 | PHASE2 | TERMINATED | Study of Preladenant for the Treatment of Neuroleptic Induced Akathisia (Study P05145) |
| NCT01385592 | PHASE2 | COMPLETED | Evaluation of the Efficacy and Safety of AFQ056 in Parkinson’s Patients With L-dopa Induced Dyskinesias |
| NCT01491529 | PHASE2 | COMPLETED | Evaluation of the Efficacy and Safety of Modified Release AFQ056 in Parkinson’s Patients With L-dopa Induced Dyskinesias |
| NCT01491932 | PHASE2 | COMPLETED | Open-label, Long-term Safety Extension Study of AFQ056 in Parkinson’s Patients With L-dopa Induced Dyskinesias |
| NCT02500628 | PHASE2 | COMPLETED | Heart Rate Variability in Response to Metformin Challenge |
| NCT04536987 | PHASE2 | COMPLETED | Robot Therapy for Rehabilitation of Hand Movement After Stroke |
| NCT04912115 | PHASE2 | SUSPENDED | Randomized, Double-Blind, Active Placebo-Controlled Study of Ketamine to Treat Levodopa-Induced Dyskinesia |
| NCT05636852 | PHASE2 | TERMINATED | Altropane Dose for Imaging Patients With Suspected Parkinson’s Disease |
| NCT00202397 | PHASE2 | COMPLETED | Effect of Riluzole as a Symptomatic Approach in Patients With Chronic Cerebellar Ataxia |
| NCT02304302 | PHASE2 | COMPLETED | Down Syndrome Memantine Follow-up Study |
| NCT03862950 | PHASE2 | COMPLETED | A Trial of Metformin in Individuals With Fragile X Syndrome (Met) |
| NCT04529226 | PHASE2 | UNKNOWN | Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis |
| NCT04821856 | PHASE2 | COMPLETED | Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability |
| NCT01689285 | PHASE1 | COMPLETED | Bioequivalence Study in Healthy Volunteers of a New Paediatric Formulation of Valacyclovir |
| NCT06409494 | PHASE1 | ACTIVE_NOT_RECRUITING | Clinical Trial to Evaluate EuHZV in Healthy Adults Aged 50 to 69 Years |
| NCT00001663 | PHASE1 | COMPLETED | Treatment of Cortical Myoclonus With Repetitive Transcranial Magnetic Stimulation |
| NCT02589340 | PHASE1 | TERMINATED | Buspirone, in Combination With Amantadine, for the Treatment of Levodopa-induced Dyskinesia |
| NCT03065192 | PHASE1 | COMPLETED | Safety and Efficacy Study of VY-AADC01 for Advanced Parkinson’s Disease |
| NCT07232147 | PHASE1 | NOT_YET_RECRUITING | Clinical Research on Stem Cell Therapy for Parkinson’s Disease |
| NCT05273320 | PHASE1 | COMPLETED | Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities |
| NCT05301361 | PHASE1 | ENROLLING_BY_INVITATION | Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities |
| NCT06016764 | PHASE1 | COMPLETED | Use of MRI and cTBS for Catatonia in Autism |
| NCT06586827 | PHASE1 | COMPLETED | Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD |
| NCT07531940 | PHASE1 | NOT_YET_RECRUITING | Escalating Doses of Memantine in Down Syndrome (MEDS-123) |
| NCT02699190 | Not specified | COMPLETED | LeukoSEQ: Whole Genome Sequencing as a First-Line Diagnostic Tool for Leukodystrophies |
Related Atlas pages
- Associated diseases: odontoleukodystrophy, Wiedemann-Rautenstrauch syndrome, leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism, hypomyelination-cerebellar atrophy-hypoplasia of the corpus callosum syndrome, tremor-ataxia-central hypomyelination syndrome, varicella zoster infection, POLR3A-related disorder
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): colorectal adenoma, hereditary ataxia, hypomyelinating leukodystrophy 4, hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism, hypomyelination-cerebellar atrophy-hypoplasia of the corpus callosum syndrome, leukodystrophy, leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism, movement disorder, odontoleukodystrophy, POLR-related leukodystrophy, POLR3A-related disorder, spastic ataxia, tremor-ataxia-central hypomyelination syndrome, varicella zoster infection, Wiedemann-Rautenstrauch syndrome