POLR1A

Chr 2ADAR

RNA polymerase I subunit A

Also known as: A190, AFDCIN, HLD27, RPA1, RPA190, RPA194, RPO1-4, RPO14

POLR1A encodes the largest catalytic subunit of RNA polymerase I, which transcribes DNA into ribosomal RNA precursors essential for ribosome biogenesis. Mutations cause acrofacial dysostosis Cincinnati type and hypomyelinating leukodystrophy, with both autosomal dominant and autosomal recessive inheritance patterns reported. This gene is highly constrained against loss-of-function variants in the general population, indicating that POLR1A variants are likely to be pathogenic when they do occur.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismAD/ARLOEUF 0.262 OMIM phenotypes
Clinical SummaryPOLR1A
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.26LOEUF
pLI 1.000
Z-score 7.50
OE 0.17 (0.110.26)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.95Z-score
OE missense 0.74 (0.700.79)
750 obs / 1014.2 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.17 (0.110.26)
00.351.4
Missense OE0.74 (0.700.79)
00.61.4
Synonymous OE0.94
01.21.6
LoF obs/exp: 16 / 94.8Missense obs/exp: 750 / 1014.2Syn Z: 1.03
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongPOLR1A-related acrofacial dysostosis, Cincinnati typeLOFAD
DN
0.3793th %ile
GOF
0.2796th %ile
LOF
0.63top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOF1 literature citation · LOEUF 0.26

Literature Evidence

LOFPolr1a loss of function led to perturbed ribosome biogenesis and p53-dependent cell death, resulting in a deficiency of neural-crest-derived skeletal precursor cells and consequently craniofacial anomalies. Our findings expand the genotypic and phenotypic heterogeneity of congenital acrofacial disorPMID:25913037

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

POLR1A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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