ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8606C>A (p.Thr2869Lys) (rs142522748)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082586 SCV000114628 benign not specified 2013-07-15 criteria provided, single submitter clinical testing
Counsyl RCV000169042 SCV000220200 likely benign Autosomal recessive polycystic kidney disease 2014-03-27 criteria provided, single submitter literature only
PreventionGenetics,PreventionGenetics RCV000082586 SCV000315846 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000169042 SCV000557642 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000082586 SCV000592905 likely benign not specified 2016-05-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587557 SCV000699883 likely benign not provided 2016-01-22 criteria provided, single submitter clinical testing Variant summary: c.8606C>A affects a conserved nucleotide, resulting in amino acid change from Thr to Lys. 3/4 in-silico tools predict this variant to be damaging, however, these in silico predictions have not been validated by any in vitro/vivo functional studies yet. This variant was found in 1133/121106 control chromosomes at a frequency of 0.0093554, predominantly observed in non-Finnish European subpopulation in ExAC with MAF of 0.01445 (962/66572 chr) with total 14 homozygotes. This frequency exceeds the maximal expected frequency of a pathogenic allele (0.0070711), suggesting this variant is a benign polymorphism in non-Finnish Europeans. Two clinical laboratories via ClinVar classified this variant as benign/likely benign. Autosomal Recessive Polycystic Kidney Disease database and multiple literature publications list this variant as polymorphism. Considering all, this variant was classified as Likely Benign until more information becomes available.
SIB Swiss Institute of Bioinformatics RCV000169042 SCV000803557 benign Autosomal recessive polycystic kidney disease 2018-05-31 criteria provided, single submitter curation This variant is interpreted as a Benign, for Polycystic kidney disease 4 with or without polycystic liver disease, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Illumina Clinical Services Laboratory,Illumina RCV000169042 SCV001323389 likely benign Autosomal recessive polycystic kidney disease 2017-04-27 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.

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