ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.7913A>G (p.His2638Arg)

gnomAD frequency: 0.19138  dbSNP: rs9936785
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000246311 SCV000305783 benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000755598 SCV000604697 benign Polycystic kidney disease, adult type 2020-07-07 criteria provided, single submitter clinical testing
Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research RCV001254267 SCV001430184 benign Autosomal dominant polycystic kidney disease 2019-01-01 criteria provided, single submitter research
GeneDx RCV001668450 SCV001889446 benign not provided 2019-12-30 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 11571556, 22008521, 22383692)
Breakthrough Genomics, Breakthrough Genomics RCV001668450 SCV005290703 benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001291878 SCV000592809 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.His2638Arg variant was identified in 56 of 674 proband chromosomes (frequency: 0.083) from individuals or families with ADPKD or renal disease, and was not identified in 100 control chromosomes from healthy individuals (Bataille 2011, Bouba 2001, McCluskey 2002, Rossetti 2012). All the studies have identified the variant as a polymorphism. The p.His2638Arg variant was identified in the dbSNP (ID: rs9936785) with unknown clinical significance with a minor allele frequency 0.1356 (679 of 5007 chromosomes in 1000 Genome Project). The variant was identified in Exome Aggregation Consortium (ExAC) database (released March 14, 2016) in 4424 of 106234 chromosomes, 501 of which are homozygous (frequency: 0.04164) or 192 of 6148 of European (Finnish), 2099 of 57384 European (Non-Finnish), 177 of 10876 Latino, 1653 of 6824 African, 228 of 16016, South Asians, 33 of 790 Other and in 42 of 8196 East Asians chromosomes. The variant was identified in PKD Mutation Database and classified as “likely neutral”; and in GeneInsight the variant was identified by one submitter and classified as benign. In Clinvitae the variant was identified by EmyClass and identified as benign. The p.His2638 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In addition this variant was identified co-occurring with a pathogenic PKD1 variant (PKD1, EXON43, c.11798_11810del, p.Leu3933ArgfsX8) in a patient with a clinical diagnosis of ADPKD. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.

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