Submissions for variant NM_003978.5(PSTPIP1):c.247+1G>A

gnomAD frequency: 0.00002  dbSNP: rs573784011

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000489936	SCV000576662	uncertain significance	not provided	2017-04-24	criteria provided, single submitter	clinical testing	The c.247+1 G>A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.247+1 G>A splice site variant in the PSTPIP1 gene destroys the canonical splice donor site in intron 4. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. However, no splicing variants in PSTPIP1 have been reported to date in the Human Gene Mutation Database, and their contribution to disease is uncertain (Stenson et al., 2014; Nesterovitch et al., 2011). Additionally, the c.247+1 G>A variant is observed in 25/16510 (0.1%) alleles from individuals of South Asian background, including one homozygote, in the ExAC dataset (Lek et al., 2016). In the absence of functional studies, the actual effect of this sequence change in this individual is unknown. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp	RCV002063830	SCV002482998	likely benign	Pyogenic arthritis-pyoderma gangrenosum-acne syndrome	2023-09-12	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000489936	SCV004137425	benign	not provided	2022-07-01	criteria provided, single submitter	clinical testing	PSTPIP1: BS1, BS2