Submissions for variant NM_001127178.3(PIGG):c.1702dup (p.Ser568fs)

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Total submissions: 3

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV002637249	SCV003513152	pathogenic	Intellectual disability, autosomal recessive 53	2024-05-12	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Ser568Lysfs*35) in the PIGG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PIGG are known to be pathogenic (PMID: 26996948, 28581210, 28771251). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIGG-related conditions. ClinVar contains an entry for this variant (Variation ID: 2194645). For these reasons, this variant has been classified as Pathogenic.
GeneDx	RCV003227087	SCV003923988	pathogenic	not provided	2023-07-24	criteria provided, single submitter	clinical testing	Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002637249	SCV005077155	pathogenic	Intellectual disability, autosomal recessive 53	2024-04-19	criteria provided, single submitter	clinical testing	Variant summary: PIGG c.1702dupA (p.Ser568LysfsX35) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4e-06 in 251228 control chromosomes. To our knowledge, no occurrence of c.1702dupA in individuals affected with Intellectual Disability, Autosomal Recessive 53 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 2194645). Based on the evidence outlined above, the variant was classified as pathogenic.

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