ClinVar Genomic variation as it relates to human health

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: 35316923, 27512013, 33726816, 34440436, 32870266, 36268624, 37273706, 27029625, 25133958, 32345981, 22855961)

ACMG classification criteria: PS4, PM3, PP3

The p.Met415Thr variant in POLR3B has been reported in 7 individuals with 4H leukodystrophy (PMID: 27512013, 25133958, 27029625, 33726816, 34440436, 31996231) and has been identified in 0.11% (149/128840) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs199504211). 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. This variant has also been reported in ClinVar (Variation ID#: 285205) and has been interpreted as VUS by Eurofins NTD (LLC) and Fulgent Genetics, and likely pathogenic or pathogenic by Institute of Human Genetics (University of Leipzig Medical Center), Institute of Medical Genetics and Applied Genomics (University Hospital Tübingen), GeneDx, and GeneReviews. Of the 7 affected individuals, 2 were compound heterozygotes that carried reported pathogenic variants in trans and with unknown phase, which increases the likelihood that the p.Met415Thr variant is pathogenic (VariationID: 620581; PMID: 31996231, 27512013). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The number of missense variants reported in POLR3B in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, the clinical significance of the p.Met415Thr variant is uncertain. ACMG/AMP Criteria applied: PP3, PM3, PP2 (Richards 2015).

Variant summary: POLR3B c.1244T>C (p.Met415Thr) results in a non-conservative amino acid change in 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 0.00055 in 251068 control chromosomes. c.1244T>C has been reported in the literature in individuals affected with POLR3-Related Leukodystrophy, cerebellar ataxia, isolated hypogonadotropic hypogonadism (Barbosa-Gouveia_2021, Fogel_2014, Richards_2017) and in an individual with clinical features of ataxia, myopia, developmental delay, short stature, and cerebellar atrophy (La Piana_2016). In all cases, the second allele reported in the patients were of unknown or uncertain significance. These reports do not provide unequivocal conclusions about association of the variant with POLR3-Related Leukodystrophy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 11 ClinVar submitters have submitted clinical-significance assessments for this variant to ClinVar after 2014. Multiple laboratories reported the variant with conflicting assessments including uncertain significance (n=5), likely pathogenic (n=4), or pathogenic (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance.

The POLR3B c.1244T>C (p.Met415Thr) missense variant has been reported in at least five individuals with variable presentations of POLR3-related conditions, including ataxia, hypogonadotropic hypogonadism, white matter abnormalities on brain MRI, and myopia (PMID: 25133958; 27029625; 27512013; 33726816; 34440436). In two of these cases, the variant co-occurred with a predicted loss of function variant, and in at least three other cases it has been reported in trans with another missense variant. The highest frequency of this allele in the Genome Aggregation Database is 0.001337 in the European (non-Finnish) population (version 3.1.2). Computational evidence suggests the variant may impact the gene or gene product. Based on the available evidence, the c.1244T>C (p.Met415Thr) variant is classified as a variant of uncertain significance for POLR3-related leukodystrophy.

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 415 of the POLR3B protein (p.Met415Thr). This variant is present in population databases (rs199504211, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of autosomal recessive POLR3B-related conditions (PMID: 25133958, 27029625, 27512013, 34440436). ClinVar contains an entry for this variant (Variation ID: 285205). 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 not expected to disrupt POLR3B protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

The c.1244T>C (p.M415T) alteration is located in exon 13 (coding exon 13) of the POLR3B gene. This alteration results from a T to C substitution at nucleotide position 1244, causing the methionine (M) at amino acid position 415 to be replaced by a threonine (T)._x000D_ _x000D_ Based on the available evidence, the c.1244T>C p.M415T alteration is classified as likely pathogenic for autosomal recessive POLR3B-related hypomyelinating leukodystrophy; however, it is unlikely to be causative of autosomal dominant POLR3B-related Charcot-Marie-Tooth disease type 1. Based on data from gnomAD, the C allele has an overall frequency of 0.06% (160/282446) total alleles studied. The highest observed frequency was 0.12% (149/128840) of European (non-Finnish) alleles. This variant has been reported to be compound heterozygous with other POLR3B variants in multiple individuals with features consistent with POLR3B-related hypomyelinating leukodystrophy (Fogel, 2014; La Piana, 2016; Richards, 2017; Barbosa-Gouveia, 2021; Gach, 2022). This amino acid position is highly conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic.

POLR3B: PM3:Strong, PM2, PP2

BS1, PP3, PM3_strong