ClinVar Genomic variation as it relates to human health

RT-PCR studies of c.2084-6A>G indicate that it creates a cryptic splice acceptor site, leading to a frameshift and a premature stop codon at position 5 of the new reading frame (Daoud et al., 2013); This variant is associated with the following publications: (PMID: 27029625, 23355746, 25339210, 26478204, 31980526)

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS3,PM2,PM3,PP3.

This sequence change falls in intron 19 of the POLR3B gene. It does not directly change the encoded amino acid sequence of the POLR3B protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs747912710, gnomAD 0.02%). This variant has been observed in individuals with leukodystrophy (PMID: 23355746, 25339210). ClinVar contains an entry for this variant (Variation ID: 419962). Studies have shown that this variant results in an abnormal splicing event, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 23355746). For these reasons, this variant has been classified as Pathogenic.

The c.2084-6A>G variant in POLR3B has been reported in 9 compound heterozygous individuals with 4H leukodystrophy (PMID: 23355746, 25339210, 26478204, 27029625, 31577365), and has been identified in 0.02% (13/128322) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs747912710). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. Of the 9 affected individuals, 5 were compound heterozygotes that carried reported pathogenic variants with unknown phase, which increases the likelihood that the c.2084-6A>G variant is pathogenic (VariationID: 31166; PMID: 23355746, 25339210, 31577365). This variant has also been reported in ClinVar (Variation ID#: 419962) and has been interpreted as pathogenic by GeneDx, Institute of Medical Genetics and Applied Genomics (University Hospital Tübingen), Centre for Mendelian Genomics (University Medical Centre Ljubljana), Institute for Clinical Genetics (University Hospital TU Dresden), and GeneReviews. In vitro functional studies provide some evidence that the c.2084-6A>G variant may impact protein function (PMID: 23355746). However, these types of assays may not accurately represent biological function. This variant is located in the 5' splice region. Computational tools do suggest an impact to splicing. However, this information is not predictive enough to determine pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive 4H leukodystrophy. ACMG/AMP Criteria applied: PM3_strong, PS3_moderate, PP3 (Richards 2015)

This variant (c.2084-6G>A) has been observed at very low frequency in population databases (gnomAD) and has been reported in the literature (PMID 23355746, PMID 27029625, PMID. 25339210, PMID 26478204). Splice prediction programs suggest a deleterious effect on correct splicing and this is supoprted by RNA analysis (PMID 23355746). The change was found in an affected individual who is also heterozygous for another likely pathogenic varaint (c.1999G>A, p.Val667Met), although no parental studies were performed.