Submissions for variant NM_018129.4(PNPO):c.347G>A (p.Arg116Gln)

gnomAD frequency: 0.04944  dbSNP: rs17679445

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000118002	SCV000229145	benign	not specified	2015-05-15	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000118002	SCV000313160	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000357367	SCV000403786	benign	Pyridoxal phosphate-responsive seizures	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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Ambry Genetics	RCV002312225	SCV000846358	benign	Inborn genetic diseases	2016-03-02	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000357367	SCV001722599	benign	Pyridoxal phosphate-responsive seizures	2025-02-04	criteria provided, single submitter	clinical testing
GeneDx	RCV001707529	SCV001935704	benign	not provided	2018-11-28	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 28818555, 28349276, 24645144, 24658933)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000118002	SCV002050722	likely benign	not specified	2021-12-03	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV001707529	SCV005212975	likely benign	not provided		criteria provided, single submitter	not provided
Genetic Services Laboratory, University of Chicago	RCV000118002	SCV000152320	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Clinical Genetics, Academic Medical Center	RCV000118002	SCV001919587	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000118002	SCV001931276	benign	not specified		no assertion criteria provided	clinical testing