ClinVar Genomic variation as it relates to human health

The p.Arg304Gln variant in AIP has been reported in >10 individuals with pituita ry adenoma and segregated with disease in two affected members across two famili es (Georgitsi 2007, Igreja 2010, Occhi 2010, Tichomirowa 2011, Cazabat 2012, Cun y 2013, Pardi 2013, Preda 2014, Schofl 2014, Arajuo 2017). This variant has also been identified in multiple individuals without pituitary lesions (Tichomirowa 2011, Freudenberg-Hua 2014, Pardi 2013) and in 2.07% (208/10074) of Ashkenazi Je wish chromosomes, including 2 homozygous individuals, by gnomAD (http://gnomad.b roadinstitute.org). However, this frequency does not rule out a pathogenic role due to the prevalence of pituitary adenoma in the general population (~11% on au topsy; Molitch 2008) and the reduced penetrance of pituitary adenoma in individu als carrying pathogenic AIP variants (15-30%; Korbonits 2018). In vitro function al studies suggest that the p.Arg304Gln variant does not have a strong impact on protein function (Georgitisi 2007, Igreja 2010, Morgan 2012); however these typ es of assays may not accurately represent biological function. Computational pre diction tools and conservation analysis do not provide strong support for or aga inst an impact to the protein. Finally, this variant is present in ClinVar with conflicting interpretations of pathogenicity (Variation ID# 4893). In summary, t he clinical significance of the p.Arg304Gln variant is uncertain. ACMG/AMP Crit eria applied: PS4_Moderate, BS3_Supporting.

The AIP c.911G>A (p.Arg304Gln) missense change has a maximum subpopulation frequency of 0.14% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function. A ß-galactosidase activity assay in yeast showed a mild reduction of ß-galactosidase activity compared to wildtype (PMID: 20506337). This variant has been reported in individuals with pituitary adenoma (PMID: 17360484, 17609395, 18381572, 19366855, 20506337). In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

AIP: BP4

The R304Q variant in the AIP gene has been reported in the literature in several patients with familial isolated pituitary adenoma, sporadic pituitary adenoma, acromegaly, and/or hyperparathyroidism (Georgitsi et al., 2007; Igreja et al., 2010; Occhi et al., 2010; Tichomirowa et al., 2011; Cazabat et al., 2012; Cuny et al., 2013; Pardi et al., 2013; Preda et al., 2014; Schofl et al., 2014). This variant is located in the aryl hydrocarbon receptor (AHR) binding region and has been hypothesized to impact AIP and AHR interactions (Georgitisi et al., 2007). However, AIP also interacts with PDE4A5 and in vitro AIP-PDE4A5 functional assays suggest that the R304Q variant only has a minimal effect on AIP-PDE4A5 binding (Igreja et al., 2010). Although the R304Q variant was not observed at any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, this variant has been observed in 3/44 (6.8%) of unaffected centenarian patients of Ashkenazi Jewish ancestry (Freudenberg-Hua et al., 2014). The R304Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the R304Q variant is damaging to the protein structure/function. Therefore, we interpret R304Q as a variant of uncertain significance.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

a variant already in ClinVar database associated with drug response in a Turkish patient

The AIP c.911G>A variant is predicted to result in the amino acid substitution p.Arg304Gln. This variant, located within a CpG mutational hotspot, has been documented in multiple individuals with sporadic and familial pituitary adenomas (Georgitsi et al. 2007. PubMed ID: 17360484; Leontiou et al. 2008. PubMed ID: 18381572; Pardi et al. 2013. PubMed ID: 23633209; Cuny et al. 2013. PubMed ID: 23321498) and in at least one family member (patient’s mother) with normal pituitary MRI (Cuny et al. 2013. PubMed ID: 23321498). It has also been reported in an individual with prolactinoma (Araujo et al. 2017. PubMed ID: 29074612) and another with acromegaly (Preda et al 2014. PubMed ID: 25184284). This variant has also been described in an extended Danish family with several members with acromegalic features and somatotropinomas (Dal et al. 2020. PubMed ID: 32324286). The disease penetrance in this family was estimated to be 6%. Potential disease-modifying variants were also identified in 2 additional genes (PDE11A and ALG14). A yeast two-hybrid study of this variant demonstrated minimally deficient wild type activity (Igreja et al. 2010. PubMed ID: 20506337), however, tumors carrying this variant have been reported to display decreased AIP expression (Pardi et al. 2013. PubMed ID: 23633209). This variant is reported in 2.1% of alleles in individuals of Ashkenazi Jewish descent, including 2 homozygote observations, in gnomAD. In ClinVar, this variant is has conflicting interpretations of ranging from benign to uncertain significance, with the majority of submitters interpreting it as uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/4893/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

a variant already in ClinVar database associated with clinical findings in a Turkish patient