ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.1030C>T (p.Arg344Ter) (rs769256568)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center,Shahid Beheshti University of Medical Sciences RCV000625901 SCV000746480 pathogenic Neu-Laxova syndrome 1 2017-12-03 criteria provided, single submitter clinical testing
Invitae RCV000798475 SCV000938093 pathogenic Phosphoglycerate dehydrogenase deficiency 2020-10-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg344*) in the PHGDH gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs769256568, ExAC 0.02%). This variant has not been reported in the literature in individuals with PHGDH-related conditions. ClinVar contains an entry for this variant (Variation ID: 522743). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in PHGDH are known to be pathogenic (PMID: 14645240, 24836451). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000625901 SCV001521892 likely pathogenic Neu-Laxova syndrome 1 2020-06-09 criteria provided, single submitter clinical testing This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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