ClinVar Miner

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

gnomAD frequency: 0.00001  dbSNP: rs769256568
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Total submissions: 7
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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
Labcorp Genetics (formerly Invitae), Labcorp RCV000798475 SCV000938093 pathogenic PHGDH deficiency 2024-04-15 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. Loss-of-function variants in PHGDH are known to be pathogenic (PMID: 14645240, 24836451). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected 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 disrupt the consensus splice site. 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].
Revvity Omics, Revvity RCV001784181 SCV002018777 pathogenic not provided 2021-03-15 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000625901 SCV004049108 likely pathogenic Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000798475 SCV004049109 likely pathogenic PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV000798475 SCV004804715 pathogenic PHGDH deficiency 2024-03-17 criteria provided, single submitter research

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