ClinVar Genomic variation as it relates to human health

Variant summary: POLR1C c.836G>A (p.Arg279Gln) results in a conservative amino acid change located in the DNA-directed RNA polymerase, RpoA/D/Rpb3-type domain (IPR011263) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0002 in 251432 control chromosomes. This frequency does not allow conclusions about variant significance. c.836G>A has been reported in the literature as homozygous and compound heterozygous genotypes in individuals affected with POLR1C-Related Disorders, specifically Treacher-Collins syndrome and in cohorts with a diagnosis of childhood cerebellar ataxia, specifically hypomyelinating leukodystrophy (example, Dauwerse_2010, Ghesh_2019, Ching-Lopez_2021). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 279 of the POLR1C protein (p.Arg279Gln). This variant is present in population databases (rs191582628, gnomAD 0.07%). This missense change has been observed in individuals with clinical features of Treacher Collins syndrome (PMID: 21131976, 30957429). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 30811). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt POLR1C protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects POLR1C function (PMID: 26151409, 29567474). For these reasons, this variant has been classified as Pathogenic.

The POLR1C c.836G>A (p.Arg279Gln) missense variant has been reported in one study in which it was identified in a compound heterozygous state in three individuals, including two siblings, with Treacher Collins syndrome (Dauwerse et al. 2011). The p.Arg279Gln was also found in a heterozygous state in four unaffected family members. The variant was absent from 272 controls but is reported at a frequency of 0.00052 in the Latino population of the Exome Aggregation Consortium. Functional studies in HeLa cell lines stably expressing wild type or p.Arg279Gln-POLR1C demonstrated that the p.Arg279Gln variant did not affect polymerase assembly but did impair the targeting of the POLR1C protein to the nucleolus, the site of Pol I transcription (Thiffault et al. 2015). Based on the evidence, the p.Arg279Gln variant is classified as likely pathogenic for Treacher Collins syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

A different missense change at this residue (R279W) has been reported as pathogenic in the published literature and at GeneDx, in association with POLR1C-related disorder (PMID: 21131976); Published functional studies demonstrate that R279Q impairs targeting of the protein to the nucleolus and inhibits chondrogenic differentiation (PMID: 29567474, 26151409); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26151409, 33558764, 35012964, 37197783, 30957429, 33804237, 31589614, 33726816, 36082953, 36271492, 21131976, 32042905, 29567474)

This variant is interpreted as a Pathogenic, for Treacher Collins syndrome 3, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2-Supporting =>PM2 downgraded in strength to Supporting. PS3 => Well-established functional studies show a deleterious effect (PMID:29567474). PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:21131976). PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:21131976). PM5 => Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before (PMID:21131976). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product.

The c.836G>A (p.R279Q) alteration is located in exon 8 (coding exon 8) of the POLR1C gene. This alteration results from a G to A substitution at nucleotide position 836, causing the arginine (R) at amino acid position 279 to be replaced by a glutamine (Q). Based on data from the Genome Aggregation Database (gnomAD) database, the POLR1C c.836G>A alteration was observed in 0.02% (54/282838) of total alleles studied, with a frequency of 0.07% (24/35440) in the Latino subpopulation. This mutation was identified in three individuals with Treacher Collins syndrome and a second POLR1C variant in trans (Dauwerse, 2011; Ghesh, 2019). It was also identified in two individuals with leukodystrophy; one individual was compound heterozygous and the other was homozygous for this mutation (Gauquelin, 2019). In COS7 and ATDC5 cells with this mutation, the protein localized to the lysosome rather than the nuclear regions (Matsumoto, 2018). The p.R279Q alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.