ClinVar Genomic variation as it relates to human health

Observed in the homozygous and heterozygous state in individuals with features of Kallman syndrome (Cole et al., 2008; Sarfati et al., 2013; Miraoui et al., 2013); Published functional studies demonstrate a damaging effect (impairment of G-protein signaling) (Sbai et al., 2014); Other functional studies indicate that while signaling is impaired, R85C does not impact cell-surface targeting or agonist affinity and likely does not exhibit a dominant negative effect (Monnier et al., 2009); 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: 23643382, 22745195, 25759380, 21858136, 20696889, 28453858, 29161432, 24031091, 34426522, 18559922, 30430143, 33098107, 34055685, 36110220, 35236788, 37338295, 20022991, 34653508, Jimenez_Ruiz_2022, 17054399, 25636053, 23082007, 24204987, 35207461, 36694982, 24830383, 18826963)

Variant summary: PROKR2 c.253C>T (p.Arg85Cys) results in a non-conservative amino acid change located in the GPCR, rhodopsin-like, 7TM domain (IPR017452) of 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 0.00059 in 251490 control chromosomes in the gnomAD database, including 2 homozygotes. This frequency does not allow conclusions about variant significance. c.253C>T has been reported in the literature in multiple individuals affected with features of Kallmann Syndrome such as normosmic idiopathic hypogonadotropic hypogonadism and has been reported among milder variants that may rely upon the genetic context for their phenotypic penetrance (example, Monnier_2009, Sarfati_2013, Moya-Plana_2013, Cox_2018). However, these report(s) do not provide unequivocal conclusions about association of the variant with Kallmann Syndrome 3. At least two publications report experimental evidence evaluating an impact on protein function (example, Monnier_2009 and Cox_2018). The most pronounced variant effect results in impaired G protein-coupling of the receptor and impaired intracellular Ca2+ increase evoked by PROK2 (Monnier_2009) as well as 30.9% of WT cAMP signaling but no effect on two other signaling pathway assays evaluated, namely MAPK and IP-one (Cox_2018). The following publications have been ascertained in the context of this evaluation (PMID: 29161432, 18826963, 23082007, 24031091). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (LP/P, n=3; VUS, n=3). At-least one of these submitters has re-classified this variant from Likely pathogenic to VUS since our initial evaluation. All submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as uncertain significance.

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 85 of the PROKR2 protein (p.Arg85Cys). This variant is present in population databases (rs141090506, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with PROKR2-related conditions (PMID: 2403109, 20022991, 30430143). ClinVar contains an entry for this variant (Variation ID: 156562). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PROKR2 protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on PROKR2 function (PMID: 18559922, 24830383, 29161432). 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.253C>T;p.(Arg85Cys) missense change has been observed in affected individual(s)(PMID: 17054399; 18559922; 18826963; 20502053; 24204987; 25636053; 30430143) - .PS4. The variant is present at low allele frequencies population databases (rs141090506– gnomAD 0.006834%; ABraOM no frequency - http://abraom.ib.usp.br/) -PM2_supporting. Pathogenic missense variant in this residue have been reported and classified as Pathogenic by ACMG criteria (PMID: 17054399; c.254G>A;p.(R85H)) - PM5. In summary, the currently available evidence indicates that the variant is Likely Pathogenic

The PROKR2 c.253C>T variant is predicted to result in the amino acid substitution p.Arg85Cys. This patient is heterozygous in the PROKR2 gene for a sequence variant defined as c.253C>T, which is predicted to result in the amino acid substitution p.Arg85Cys. This variant has been reported in the heterozygous state in multiple patients with Kallmann syndrome, normosmic hypogonadotropic hypogonadism, or combined pituitary hormone deficiencies (Cole et al. 2008. PubMed ID: 18559922; Monnier et al. 2009. PubMed ID: 18826963; Sykiotis et al. 2010. PubMed ID: 20696889, Table S01 and S02; Miraoui et al. 2013. PubMed ID: 23643382, Table S3; Sarfati et al. 2013. PubMed ID: 24031091; Correa et al. 2015. PubMed ID: 25759380; McCormack et al. 2017. PubMed ID: 28453858). However, this variant has also been reported in healthy first-degree relatives of Kallmann probands and healthy controls (Ruiz-Ferrer et al. 2011. PubMed ID: 21858136; Sarfati et al. 2013. PubMed ID: 24031091; McCormack et al. 2017. PubMed ID: 28453858). In vitro functional studies indicated that the p.Arg85Cys variant could impair G protein coupling of the receptor and moderately compromises receptor signaling through both MAPK and Ca2+ pathways (Cole et al. 2008. PubMed ID: 18559922; Monnier et al. 2009. PubMed ID: 18826963; Sbai et al. 2014. PubMed ID: 24830383). However, other studies showed that the p.Arg85Cys was benign in 2 out of 3 signaling pathways when tested alone, and the p.Arg85Cys variant could be rescued by the presence of WT PROKR2 in cAMP signaling pathway during co-transfection of wild-type and p.Arg85Cys PROKR2, suggesting this variant might be a milder variant that may rely upon the genetic context for its phenotypic penetrance (Cox et al. 2018. PubMed ID: 29161432, Table S2 and Table 1). A few different variants affecting the same amino acid (p.Arg85Gly, p.Arg85Leu and p. Arg85His) have been reported in association with Kallmann syndrome (Human Gene Mutation Database, HGMD; http://www.hgmd.cf.ac.uk/). Of note, while the vast majority of PROKR2 variants associated with hypogonadotropic hypogonadism are heterozygous with no evident mutation on the second allele, biallelic loss-of-function variants in PROKR2 have also been described in association with autosomal recessive hypogonadotropic hypogonadism (Dodé et al. 2006. PubMed ID: 17054399; Cole et al. 2008. PubMed ID: 18559922; Abreu et al. 2008. PubMed ID: 18682503; Tommiska et al. 2013. PubMed ID: 23200691). This variant is reported in 0.22% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.