ClinVar Genomic variation as it relates to human health

Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Published functional studies suggest a damaging effect: non-detectable DBH production (Kim et al., 2011); This variant is associated with the following publications: (PMID: 21209083, 14598346, 31980526, 11857564, 15060114, 21471955, 20301647, 31589614, 27778639)

The 339+2T>C variant in DBH has been previously reported in 1 homozygous and 5 compound heterozygous individuals with dopamine beta-hydroxylase deficiency and was found to segregate with disease in 2 affected compound heterozygous relatives (Kim 2002, Denium 2004, Kim 2011, ). This variant has been identified in 0.128% (11/8600) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs74853476). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and in vitro splicing assays suggest it causes altered splicing leading to an absent protein (Kim 2011); however, these types of assays may not accurately represent biological function. In summary, this variant meets our criteria to be classified as pathogenic for dopamine beta-hydroxylase deficiency in an autosomal recessive manner (http://pcpgmwww.partners.org/personalizedmedicince/LMM ) based upon segregation studies and functional evidence.

The DBH c.339+2T>C variant, also referred to as IVS1+2T>C, occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. Across five studies, this variant is reported in a total of 11 dopamine beta-hydroxylas (DBH) deficiency patients, including two homozygotes and nine compound heterozygotes (Kim et al. 2002; Zabetian et al. 2003; Deinum et al. 2004; Kim et al. 2011; Jepma et al. 2011). The variant was also found in a heterozygous state in ten unaffected individuals and family members of patients. The c.339+2T>C variant was reported in a heterozygous state in one of 989 total controls and is reported at a frequency of 0.00128 in the European American population of the Exome Sequencing Project. RT-PCR analysis of the variant mRNA expressed in COS-7 cells showed that the c.339+2T>C variant caused aberrant splicing that resulted in a transcript that included intronic sequence and a premature termination codon (Kim et al. 2002). Additionally, Kim et al. (2011) demonstrated that expression of the c.339+2T>C variant in CHO cells showed no detectable DBH protein. Based on the collective evidence, the c.339+2T>C variant is classified as pathogenic for dopamine beta-hydroxylase deficiency. 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]. This variant has been previously reported as disease-causing [PMID 11857564, 27778639, 21209083]

Variant summary: DBH c.339+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: three predict the variant abolishes a 5' splicing donor site, and one predicts the variant weakens a 5' donor site. At least one publication reports experimental evidence that this variant results in aberrant mRNA splicing leading to the introduction of a premature stop codon (e.g., Kim_2002). The variant allele was found at a frequency of 0.00072 in 238286 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.339+2T>C has been reported in the literature in both homozygous and compound heterozygous individuals affected with Orthostatic Hypotension 1 (e.g., Kim_2002, Deinum_2004). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 15060114, 11857564). Six submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change affects a donor splice site in intron 1 of the DBH gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs74853476, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individuals with dopamine beta-hydroxylase deficiency (PMID: 11857564, 15060114, 21209083, 27778639). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS1+2T>C. ClinVar contains an entry for this variant (Variation ID: 1750). Studies have shown that disruption of this splice site results in abnormal mRNA splicing and introduces a premature termination codon (PMID: 11857564, 21209083). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

The c.339+2T>C variant in DBH has previously been reported in individuals with dopamine beta hydroxylase deficiency [PMID: 11857564, 15060114, 23622564, 27778639], and it has been deposited in ClinVar [ClinVar ID: 1750]. The c.339+2T>C variant is observed in 503 alleles (~0.09% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.339+2T>C variant in DBH is located in the canonical splice donor site of exon 1 of this 11 exon gene, and predicted to result in loss of splice donor site [splice AI= 0.5854]. In vitro studies demonstrated the c.339+2T>C (previously IVS1+2T>C) variant results in absent protein [PMID: 21209083]. Based on available evidence this homozygous c.339+2T>C variant identified in DBH is classified as Pathogenic.

Common pathogenic variant that causes abnormal splicing [Kim et al 2002, Deinum et al 2004, Kim et al 2011, Phillips et al 2013, Arnold et al 2017]