Submissions for variant NM_000551.4(VHL):c.598C>T (p.Arg200Trp)

gnomAD frequency: 0.00010  dbSNP: rs28940298

Total submissions: 19

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000002320	SCV000053268	pathogenic	Chuvash polycythemia	2020-11-23	criteria provided, single submitter	clinical testing	Variant summary: VHL c.598C>T (p.Arg200Trp) results in a non-conservative amino acid change located in the von Hippel-Lindau disease tumour suppressor, alpha domain (IPR024048) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00021 in 251358 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in VHL causing Congenital Polycythemia (0.00021 vs 0.02), allowing no conclusion about variant significance. c.598C>T has been reported in the literature, primarily in the homozygous state, in multiple individuals affected with autosomal recessive Congenital Polycythemia, also referred to as familial erythrocytosis type 2 (Chuvash polycythemia) (e.g. Ang_2002, Pastore_2003, Percy_2003, Perrotta_2006). These data indicate that the variant is very likely to be associated with Congenital Polycythemia. In the heterozygous state, the variant is not expected to cause Von Hippel-Lindau Syndrome, as reported by multiple studies (e.g. Ang_2002, Pastore_2003, Gordeuk_2004, Miasnikova_2011). Experimental evidence demonstrated the variant reduced the affinity of VHL for HIF1-alpha, resulting in a reduced rate of ubiquitination under non-hypoxic conditions (Ang_2002). Five ClinVar submitters (evaluation after 2014) cite the variant as pathogenic and one ClinVar submitter (evaluation after 2014) cites it as uncertain significance. Additionally, two ClinVar submitters (evaluation after 2014) cite it as likely benign for the condition of von Hippel-Lindau syndrome. Based on the evidence outlined above, the variant was classified as pathogenic for Congenital Polycythemia (familial erythrocytosis type 2).
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000161094	SCV000205377	uncertain significance	not provided	2023-02-02	criteria provided, single submitter	clinical testing	The p.Arg200Trp variant in VHL has not been reported in the heterozygous state in individuals with paragangliomas, pheochromocytomas, or von Hippel-Lindau syndrome (Ang 2002 PMID: 12415268, Pastore 2003 PMID: 12393546, Gordeuk 2004 PMID: 14726398, Miasnikova 2011 PMID: 21606165) or in individuals with haemangioblastoma (Woodward 2007 PMID: 17264095). However, it is a well-established pathogenic variant in the homozygous state for autosomal recessive familial erythrocytosis, also known as Chuvash polycythemia (Ang 2002 PMID: 12415268, Gordeuk 2004 PMID: 14726398, Perrota 2006 PMID: 16210343, Mallik 2019 PMID: 31132167). It has also been identified in 0.065% (20/30604) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 2232). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Arg200Trp variant is uncertain as it relates to paragangliomas, pheochromocytomas, and von Hippel-Lindau syndrome. ACMG/AMP Criteria applied: PM2_Supporting.
GeneDx	RCV000161094	SCV000211829	pathogenic	not provided	2024-06-27	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect: mice homozygous for variant showed similar phenotype to patients homozygous for the variant (PMID: 17992257); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; While this variant is considered pathogenic for autosomal recessive Chuvash polycythemia, there is no evidence that it causes increased risk for von Hippel Lindau disease (PMID: 12393546, 12844285, 17264095, 21606165); This variant is associated with the following publications: (PMID: 27568332, 15574766, 25637381, 21876117, 21993671, 27518686, 11987242, 29489754, 33033909, 31132167, 35220195, 19030229, 23015148, 18836774, 24728327, 8956040, 25371412, 12415268, 21606165, 23403324, 9829912, 27651169, 12844285, 12393546, 14726398, 28400504, 28104701, 26556299, 29741264, 29790589, 16210343, 19494350, 31568062, 12702509, 30787465, 35142155, 34308104, 35767051, 17264095, 17992257, 38390862, 37317877, 37553354, 37833987, 36744932, 37946251)
Invitae	RCV000627742	SCV000253857	pathogenic	Chuvash polycythemia; Von Hippel-Lindau syndrome	2024-01-31	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 200 of the VHL protein (p.Arg200Trp). This variant is present in population databases (rs28940298, gnomAD 0.07%). This variant has been observed in a family affected with von Hippel-Lindau syndrome without pheochromocytoma (PMID: 8956040), however, several studies have reported that this variant does not cause von Hippel-Lindau syndrome (PMID: 14726398, 21606165). It has also been observed to segregate with disease in related individuals. This variant is a known common cause of autosomal recessive, familial erythrocytosis type 2 (Chuvash polycythemia) in the Chuvash population of Russia and the Italian island of Ischia (PMID: 11987242, 19494350, 9058738, 16210343). In the Chuvash population, an estimated 1/20 individuals is a carrier of this variant (PMID: 12415268), while the worldwide carrier frequency is lower (rs28940298, 0.06%). ClinVar contains an entry for this variant (Variation ID: 2232). 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: 12415268, 15574766, 17992257, 19030229). For these reasons, this variant has been classified as Pathogenic.
Counsyl	RCV000148922	SCV000488867	likely benign	Von Hippel-Lindau syndrome	2016-08-16	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000574264	SCV000664473	pathogenic	Hereditary cancer-predisposing syndrome	2022-03-31	criteria provided, single submitter	clinical testing	The p.R200W pathogenic mutation (also known as c.598C>T), located in coding exon 3 of the VHL gene, results from a C to T substitution at nucleotide position 598. The arginine at codon 200 is replaced by tryptophan, an amino acid with dissimilar properties. The p.R200W alteration has been established as a founder mutation known to cause autosomal recessive Chuvash polycythemia, a condition characterized by increased red blood cell mass and high risk of peripheral thrombosis and cerebrovascular events (Ang SO et al. Nat. Genet. 2002 Dec;32:614-21; Liu E et al. Blood. 2004 Mar;103:1937-40; Gordeuk VR et al. Blood. 2004 May;103:3924-32; Tomasic NL et al. Haematologica. 2013 Apr;98(4):560-7). Functional studies on this alteration have yielded varying results on different aspects of VHL function linked to tumor formation or erythropoeisis, such as increased angiogenesis and increased hypoxia-inducible factor (HIF1a and HIF2a) expression, but retention of interaction with Elongin C (Ang SO et al. Nat. Genet. 2002 Dec;32:614-21; Rathmell WK et al. Cancer Res. 2004 Dec;64:8595-603; Hickey MM et al. J. Clin. Invest. 2007 Dec;117:3879-89; Hacker KE et al. PLoS ONE. 2008 Nov;3:e3801; Gordeuk VR et al. Blood. 2011 Nov;118:5278-82; Couvé S et al. Cancer Res. 2014 Nov;74:6554-64). Although two unrelated individuals with isolated hemangioblastoma have been reported as p.R200W heterozygotes, the vast majority of carriers are not affected with von Hippel Lindau (VHL) lesions (Pastore Y et al. Am. J. Hum. Genet. 2003 Aug;73:412-9; Woodward ER et al. Brain. 2007 Mar;130(Pt 3):836-42). In addition, one family with a clinical diagnosis of VHL was initially reported as being heterozygous for p.R200W (Olschwang S et al. Hum. Mutat. 1998;12:424-30); however, further studies of this family found that they actually carried two VHL alterations in cis (p.R200W and p.R161Q) (Couvé S et al. Cancer Res. 2014 Nov;74:6554-64). By evaluating structural stability in areas of domain interaction, pVHL-HIF1a binding ability, and expression gradients of genes regulated by VHL, the authors were able to demonstrate that the impact of the double mutant allele was more disruptive to structural and functional roles of VHL than the impact of either alteration alone. They proposed that the p.R200W alteration was not sufficient in causing classic VHL disease. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, p.R200W is interpreted as a disease-causing mutation. At this time, individuals who are heterozygous for the p.R200W alteration can be interpreted as carriers for Chuvash polycythemia; however, it is unlikely that this alteration causes von Hippel Lindau disease.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	RCV000722031	SCV000853208	pathogenic	Acute leukemia of ambiguous lineage	2017-01-20	criteria provided, single submitter	clinical testing	This is a missense alteration in which a C is replaced by a T at coding nucleotide 598 and is predicted to change an Arginine to a Tryptophan at amino acid codon 200. Classification criteria: PS1 (associated with Chuvash syndrome, only in homozygous state), PS3, PM2, PP3.
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	RCV000148922	SCV000897856	likely benign	Von Hippel-Lindau syndrome	2018-08-01	criteria provided, single submitter	clinical testing
Clinical Genetics and Genomics, Karolinska University Hospital	RCV000161094	SCV001449948	pathogenic	not provided	2019-02-14	criteria provided, single submitter	clinical testing
Mendelics	RCV002247239	SCV002519954	pathogenic	Nonpapillary renal cell carcinoma	2022-05-04	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000122262	SCV002760273	uncertain significance	not specified	2024-07-31	criteria provided, single submitter	clinical testing
Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust	RCV000002320	SCV003853410	pathogenic	Chuvash polycythemia	2023-03-23	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000148922	SCV004841671	uncertain significance	Von Hippel-Lindau syndrome	2024-02-05	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 200 of the VHL protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). **Functional studies have reported that this variant partially impacted VHL functions to varying degrees in binding and ubiquitination of HIF1alpha and the regulation of genes in the VHL-HIF and VHL-JAK2 pathways (PMID: 12415268, 15574766, 17992257, 19304954, 21685897) and partial to no impact on VHL binding to Elongin B, Elongin C, cullen and ROC/Rbx1 (PMID: 15574766, 19030229). Homozygous and compound heterozygous carriers of this variant have been reported in individuals affected with recessive Chuvash polycythemia and/or erythrocytosis (PMID: 11987242, 12415268, 12393546, 12702509, 12844285, 14726398, 15642664, 16210343, 23403324, 31132167), and haplotype analysis has found that one haplotype with this variant is a founder mutation for recessive Chuvash polycythemia (PMID: 14604959). However, these individuals and heterozygous family members are not known to exhibit multiple CNS and retinal hemangioblastomas and clear cell renal cell carcinomas that are characteristic of VHL hereditary cancer predisposition syndrome. One carrier family that was originally reported to be affected with isolated central nervous system hemangioblastoma (PMID: 17264095) was found to have this variant, p.Arg200Trp, in cis with p.Arg161Gln, and the haplotype of both variants in cis and in heterozygous state segregated with family members affected with CNS and retinal hemangioblastoma, clear cell renal cell carcinoma, pheochromocytoma and pancreatic neuroendocrine tumor (PMID: 25371412). Furthermore, functional study found that both variants in cis has an additive deleterious impact on VHL function in HIF1alpha peptide binding and deregulated expression of genes in the VHL-HIF pathway, suggesting the that the haplotype with both variants in cis is associated with autosomal dominant cancer predisposition (PMID: 25371412). This variant is common and has been identified in 57/282754 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, the heterozygous state for this variant per se may not be associated with the autosomal dominant VHL hereditary cancer predisposition syndrome. Therefore, this variant is classified as a Variant of Uncertain Significance.
OMIM	RCV000002320	SCV000022478	pathogenic	Chuvash polycythemia	2011-06-19	no assertion criteria provided	literature only
ITMI	RCV000122262	SCV000086487	not provided	not specified	2013-09-19	no assertion provided	reference population
CSER _CC_NCGL, University of Washington	RCV000148922	SCV000190679	likely benign	Von Hippel-Lindau syndrome	2014-06-01	no assertion criteria provided	research
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	RCV000002320	SCV000264776	pathogenic	Chuvash polycythemia	2016-02-26	no assertion criteria provided	clinical testing
GenomeConnect, ClinGen	RCV000148922	SCV002074976	not provided	Von Hippel-Lindau syndrome		no assertion provided	phenotyping only	Variant interpreted as Pathogenic and reported on 10-29-2020 by Lab or GTR ID 507401. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)	RCV000002320	SCV003927919	likely pathogenic	Chuvash polycythemia	2023-04-01	no assertion criteria provided	clinical testing