Submissions for variant NM_006031.6(PCNT):c.4354G>A (p.Gly1452Arg)

gnomAD frequency: 0.00149  dbSNP: rs143796569

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000328533	SCV000194487	benign	not specified	2015-11-17	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000328533	SCV000331569	benign	not specified	2016-03-03	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001001913	SCV000436995	benign	Microcephalic osteodysplastic primordial dwarfism type II	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.
GeneDx	RCV000328533	SCV000514058	likely benign	not specified	2016-07-14	criteria provided, single submitter	clinical testing	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000879337	SCV001022359	benign	not provided	2025-01-28	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001001913	SCV001159667	likely benign	Microcephalic osteodysplastic primordial dwarfism type II	2023-11-22	criteria provided, single submitter	clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV001258292	SCV001435225	benign	Intellectual disability		criteria provided, single submitter	research	The heterozygous p.Gly1452Arg variant in PCNT has been identified in the compound heterozygous state in an individual with intellectual disability (PMID: 23033978), but has also been identified in >1% of South Asian chromosomes and 3 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for intellectual disability.
Fulgent Genetics, Fulgent Genetics	RCV001001913	SCV002800264	likely benign	Microcephalic osteodysplastic primordial dwarfism type II	2021-07-21	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000879337	SCV004152021	benign	not provided	2024-04-01	criteria provided, single submitter	clinical testing	PCNT: BP4, BS1, BS2
Breakthrough Genomics, Breakthrough Genomics	RCV000879337	SCV005208843	likely benign	not provided		criteria provided, single submitter	not provided