ClinVar Genomic variation as it relates to human health

The NM_000551.4(VHL):c.500G>A (p.Arg167Gln) variant in VHL is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 167. This missense mutation has been identified in at least 19 unrelated individuals with von Hippel-Lindau disease. Mostly VHL Type 2 or 2B phenotypes are noted. However, some publications describe VHL Type 1 as well. PMIDs used: 20846682, 8707293, 9829912, 9829911, 7728151, 12114495, 12624160, 14722919. CIViC EIDs used (https://civicdb.org): 5485, 5354, 5264, 5062, 4913, 5487, 5546, 6118. 2 participating commercial laboratories reported >7 and >20 cases. The number of proband and/or family cases fulfills the criteria for strong evidence (PS4). Multiple publications (PMID: 15574766, PMID: 19030229) support disruption of Elongin C binding with the Arg167Gln variant, as well as altered regulation of HIF2a and near wild type regulation via ubiquitination of HIF1a (PS3_Supporting). A de novo (and mosaic ~5.5% allele freq in blood and ~34% in a pheochromocytoma at ~80% tumor purity) case was identified in a 16yo with no family history of VHL and fulfilling Danish Criteria for VHL (The 16yo had the following: Hb, pheochromocytoma, pancreatic endocrine tumor, left adrenal nodule). PMID: 30731206, CIViC evidence ID: EID7714. 1 commercial laboratory reports a de novo case in a child with bilateral retinal hemangiomas in the age range of 10yo (PM6). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). Arg167 is one of the germline hotspots outlined by the VHL VCEP, and it is in the Elongin binding domain (PM1). The computational predictor REVEL gives a score of 0.874, which is above the threshold of >=0.664, evidence that correlates with impact to VHL function (PP3). Per VHL VCEP specifications, this code is applied when the REVEL score is >=0.6. (PP3). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal-dominant von Hippel-Lindau disease (VHL disease) based on the ACMG/AMP criteria applied, as specified by the ClinGen VHL VCEP Version 1.0 (Specifications approval date: 02/26/2024. Variant Approval Date 06/25/2024).

The p.Arg167Gln variant in VHL (also described as p.Arg238Gln in the literature) has been reported in >15 individuals with von Hippel-Lindau syndrome (VHL) and is associated with a high incidence of pheochromocytomas (Crossey 1994, Neumann 2002, Park 2015, Sriphraprandang 2017; Zhuo 2010; Zbar 1996). It has also been r eported by other clinical laboratories in ClinVar (Variant ID: 2216). In vitro f unctional studies provide some evidence that the p.Arg167Gln variant may impact protein function (Rathmell 2004, Couve 2014). This variant has been identified i n 1/111702 European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Co mputational prediction tools and conservation analysis suggest that the p.Arg176 Gln variant may impact the protein. Of note, other variants at this position (p. Arg167Gly, p.Arg167Leu, p.Arg167Trp) have been reported in individuals with VHL, suggesting that an alteration at this position is not tolerated. In summary, th is variant meets criteria to be classified as pathogenic for VHL in an autosomal dominant manner based upon multiple occurrences in affected individuals, very l ow frequency in the general population, presence of other pathogenic variants at the same amino acid position and computational and functional evidence. ACMG/AM P criteria applied: PS4, PM2, PM5, PS3_Supporting, PP3.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 167 of the VHL protein (p.Arg167Gln). This variant is present in population databases (rs5030821, gnomAD 0.0009%). This missense change has been observed in individual(s) with pheochromocytoma, hemangioblastoma of the central nervous system and spinal cord, renal cell carcinoma, and pancreatic cyst (PMID: 7987306, 8956040, 10567493, 12000816, 15300849, 19464396). It has also been observed to segregate with disease in related individuals. This variant is also known as p.Arg238Gln. ClinVar contains an entry for this variant (Variation ID: 2216). 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 expected to disrupt VHL protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects VHL function (PMID: 15574766, 19030229, 19252526, 19602254). This variant disrupts the p.Arg167 amino acid residue in VHL. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7987306, 8730290). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The p.R167Q pathogenic mutation (also known as c.500G>A), located in coding exon 3 of the VHL gene, results from a G to A substitution at nucleotide position 500. The arginine at codon 167 is replaced by glutamine, an amino acid with highly similar properties. This mutation has been described in numerous VHL families from various ethnic backgrounds (Zbar B et al. Hum. Mutat. 1996;8:348-57; Gläsker S et al. J. Neurol. Neurosurg. Psychiatr. 1999 Dec;67:758-62; Zhou J et al. Pathol. Int. 2010 Jun;60:452-8; Lee JS et al. BMC Med. Genet. 2016 Jul;17:48; Wang X et al. Urology. 2014 Mar;83:675.e1-5; Pandit R et al. Eur. J. Endocrinol. 2016 Oct;175:311-23; Wong M et al. Chin J Cancer. 2016 Aug;35:79). Furthermore, substitutions at codon 167 impact a highly-conserved protein surface residue and have been reported to confer high pheochromocytoma risk (Crossey PA et al. Hum. Mol. Genet. 1994 Aug;3:1303-8; Cybulski C et al. J. Med. Genet. 2002 Jul;39:E38; Ong KR et al. Hum. Mutat. 2007 Feb;28:143-9). Of note, this mutation has also been reported in some literature as p.R238Q ( c.713G>A). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

R167Q (c.500G>A) is a pathogenic variant for Von Hippel-Lindau. R167Q is the most common mutation associated with Von Hippel-Lindau syndrome. This variant is very rare in the general population at 4.061e-6 in the gnomAD exomes (v2.0.2) proving ACMG code PM2. The variant occurs within the functional domain, disrupting VHL binding to elongin C (ACMG code PM1). Additional codes are provided by the following EIDs. 4913 (PS4), 5062 (PP4), 5264 (PS4), 5354 (PP4), 5487 and 4913 (PP1).

Published functional studies demonstrate a damaging effect: disrupts HIF1-alpha hypoxia responsive regulation and impairs binding with Elongin C resulting in partial or unstable pVHL E3 (VBC) complex formation (Rathmell et al., 2004; Hacker et al., 2008; Lee et al., 2009); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.713G>A, p.(R238Q); This variant is associated with the following publications: (PMID: 21528828, 24352051, 18836774, 20151405, 19030229, 23990666, 29124493, 29616089, 11354926, 31447099, 19602254, 15574766, 12000816, 25371412, 7987306, 12114495, 17661816, 12202531, 21386872, 22517557, 19464396, 24581539, 24301059, 19215943, 25562111, 15300849, 24712571, 17264095, 9106522, 19252526, 25563310, 27539324, 27527340, 7784063, 28114281, 8730290, 28469506, 8956040, 10567493, 17024664, 20518900, 10205047, 29871882, 11510758, 29625052, 32742360, 33745191, 34122352, 32561571, 30787465, 35260109, 34923986)

The missense variant c.500G>A(p.Arg167Gln) in VHL gene has been observed in heterozygous state in multiple individual(s) with pheochromocytoma and VHL related disorders (Fagundes et. al., 2019; Tung et. al., 2022; Ciotti et. al., 2009). It has also been observed to segregate with disease in related individuals. Experimental studies have shown that this missense change affects VHL function (Bangiyeva et. al., 2009). The p.Arg167Gln variant is novel (not in any individuals) in 1000 Genomes and has allele frequency of 0.0004% in gnomAD exomes database. This variant has been reported to the ClinVar database as Uncertain Significance / Pathogenic (multiple submitters). The amino acid change p.Arg167Gln in VHL is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 167 is changed to a Gln changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.