Submissions for variant NM_138694.4(PKHD1):c.2027C>G (p.Pro676Arg) (rs115045643)

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics	RCV000082533	SCV000114575	benign	not specified	2013-04-15	criteria provided, single submitter	clinical testing
Counsyl	RCV000169044	SCV000220202	likely benign	Autosomal recessive polycystic kidney disease	2014-03-27	criteria provided, single submitter	literature only
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics	RCV000224258	SCV000281335	likely benign	not provided	2015-10-29	criteria provided, single submitter	clinical testing	Converted during submission to Likely benign.
Invitae	RCV000169044	SCV000291327	benign	Autosomal recessive polycystic kidney disease	2019-12-31	criteria provided, single submitter	clinical testing
PreventionGenetics,PreventionGenetics	RCV000082533	SCV000315782	benign	not specified		criteria provided, single submitter	clinical testing
GeneDx	RCV000082533	SCV000520871	likely benign	not specified	2016-09-28	criteria provided, single submitter	clinical testing	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Integrated Genetics/Laboratory Corporation of America	RCV000224258	SCV000699854	likely benign	not provided	2016-04-26	criteria provided, single submitter	clinical testing	Variant summary: Variant affects a non-conserved nucleotide a results in a replacement of a medium size and hydrophobic Proline (P) with a large size and basic Arginine (R). in silico tools predict the variant to be normal; however these predictions have yet to be confirmed by functional studies. The variant was observed predominantly in the African subcohorts of the ExAC project at an allele frequency of 2.3% (including 3 homozygotes) which exceeds ~3 times the maximal expected allele frequency of a disease causing PKHD1 allele (0.7%) indicating the variant to be in the neutral spectrum. The variant was reported in two autosomal-recessive polycystic kidney disease patients in compound heterozygosity with a potentially pathogenic PKHD1 variant. Clinical laboratories classify variant as Benign/Likely benign via ClinVar (without evidence to independently evaluate). Considering all evidence, the variant was classified as Likely Benign.
Mendelics	RCV000169044	SCV001137147	benign	Autosomal recessive polycystic kidney disease	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Clinical Services Laboratory,Illumina	RCV000169044	SCV001325524	likely benign	Autosomal recessive polycystic kidney disease	2017-04-28	criteria provided, single submitter	clinical testing	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.