ClinVar Genomic variation as it relates to human health

Variant summary: NAGLU c.889C>T (p.Arg297X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. A truncation downstream of this position, c.1597C>T (p.Arg533X) has been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 5.8e-05 in 277224 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in NAGLU causing Mucopolysaccharidosis Type IIIB (Sanfilippo Syndrome B) (5.8e-05 vs 0.0025), allowing no conclusion about variant significance. The variant, c.889C>T, has been reported in the literature in multiple individuals affected with Mucopolysaccharidosis Type IIIB (Sanfilippo Syndrome B)(Bunge_1999, Heron_2010). 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. Five ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) ctie the variant as "likely pathogenic/pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.

The NAGLU c.889C>T (p.Arg297Ter) variant is a stop-gained variant and has been reported in at least eight studies in which it is found in a total of 26 individuals with mucopolysaccharidosis, type III including three in a homozygous state, 20 in a compound heterozygous state, and three in a heterozygous state where the second allele was not identified (Zhao et al. 1996; Beesley et al. 1998; Weber et al. 1999; Yogalingham et al. 2000; Valstar et al. 2010; de Ruijter et al. 2012; Pollard et al. 2013; Welling et al. 2015). The p.Arg297Ter variant was absent from 80 control alleles but is reported at a frequency of 0.00002 in the Total population of the Exome Aggregation Consortium. Functional studies demonstrated that the variant resulted in very low levels of NAGLU enzyme activity and a 12-fold increase in glycosaminoglycan storage in individual fibroblasts compared to normal fibroblasts (Yogalingham et al. 2000). Due to the potential impact of stop-gained variants and the supporting evidence from the literature, the p.Agr297Ter variant is classified as pathogenic for mucopolysaccharidosis, type III. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

PVS1, PS3, PM2

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.006%). Stop-gained (nonsense) is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000001562). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

Reported as a common pathogenic variant in association with MPSIIIB (Pollard et al., 2013); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate when R297X is expressed in CHO-K1 cells, only a truncated polypeptide that is rapidly degraded is observed, suggesting that the variant transcript undergoes nonsense-mediated mRNA decay, and no detectable enzyme activity is present (Yogalingam et al., 2000); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23084433, 25525159, 20852935, 9832037, 8650226, 29979746, 29620724, 9443875, 11068184, 22976768, 26907177, 10094189, 25256447, 28751108, 28836185, 32578945, 31980526)

This sequence change creates a premature translational stop signal (p.Arg297*) in the NAGLU gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NAGLU are known to be pathogenic (PMID: 9832037, 10094189, 16151907). This variant is present in population databases (rs104894592, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with mucopolysaccharidosis type III (PMID: 22976768, 28836185). ClinVar contains an entry for this variant (Variation ID: 1562). For these reasons, this variant has been classified as Pathogenic.