ClinVar Miner

Submissions for variant NM_005859.5(PURA):c.123_146del (p.Gly42_Gly49del) (rs750397204)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000548116 SCV000655464 likely benign Mental retardation, autosomal dominant 31 2020-05-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001358641 SCV001554435 likely benign not provided no assertion criteria provided clinical testing The PURA p.Gly42_Gly49del variant was not identified in the literature but was identified in dbSNP (ID: rs1014354489) and ClinVar (classified as likely benign by Invitae). The variant was identified in control databases in 5 of 35864 chromosomes at a frequency of 0.0001394 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 2 of 1530 chromosomes (freq: 0.001307) and European (non-Finnish) in 3 of 18170 chromosomes (freq: 0.000165), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), or Other populations. This is greater than the expected frequency for the severe, early-onset autosomal dominant PURA-Related Neurodevelopmental Disorders. This variant is an in-frame deletion resulting in the removal of glycine (gly) residues from codon 42 to 49; the impact of this alteration on PURA protein function is not known however this occurs within a glycine repeat region. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
GeneDx RCV001358641 SCV001791062 likely benign not provided 2018-12-10 no assertion criteria provided clinical testing

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