ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.682G>T (p.Gly228Trp)

gnomAD frequency: 0.00083  dbSNP: rs139063843
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000705685 SCV000834694 likely benign PHGDH deficiency 2024-01-24 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712537 SCV000843052 uncertain significance not provided 2018-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000705685 SCV001257743 uncertain significance PHGDH deficiency 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV001270114 SCV001448967 uncertain significance Neu-Laxova syndrome 1 2019-06-19 criteria provided, single submitter clinical testing
GeneDx RCV000712537 SCV003918756 uncertain significance not provided 2023-02-26 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33758422)
PreventionGenetics, part of Exact Sciences RCV003907959 SCV004719138 likely benign PHGDH-related disorder 2022-09-07 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000705685 SCV001463182 uncertain significance PHGDH deficiency 2019-11-11 no assertion criteria provided clinical testing

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