ClinVar Miner

Submissions for variant NM_006214.4(PHYH):c.734G>A (p.Arg245Gln) (rs62619919)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000179914 SCV000232234 benign not specified 2014-11-08 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000179914 SCV000311433 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000179914 SCV000521053 likely benign not specified 2016-02-22 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.
Counsyl RCV000665931 SCV000790142 likely benign Phytanic acid storage disease 2017-03-06 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000665931 SCV000845255 uncertain significance Phytanic acid storage disease 2018-08-07 criteria provided, single submitter clinical testing
Invitae RCV000950185 SCV001096473 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000665931 SCV001264065 uncertain significance Phytanic acid storage 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Broad Institute Rare Disease Group, Broad Institute RCV001258288 SCV001435215 benign Vitamin D-dependent rickets type II with alopecia criteria provided, single submitter research The p.Arg245Gln variant in PHYH has been identified in cis with p.Asp177Gly and in 4 individuals with Refsum disease, including 2 homozygotes and 2 heterozygotes (PMID: 10767344), and has been identified in >2% of European (Finnish) chromosomes and 9 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In vitro functional studies provide some evidence that the p.Arg245Gln variant may not impact protein function (PMID: 10767344). However, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as benign for autosomal recessive Refsum disease.
University of Washington Center for Mendelian Genomics, University of Washington RCV000755125 SCV000882947 likely pathogenic Nonsyndromic cleft lip palate 2016-03-27 no assertion criteria provided research

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