ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.9278C>G (p.Ser3093Trp) (rs374857206)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485741 SCV000574082 uncertain significance not provided 2017-03-18 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PCNT gene. The c.9278 C>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.9278 C>G variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Several in-silico splice prediction models predict that c.9278 C>G creates or enhances a cryptic donor site which may supplant the natural donor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. If the c.9278 C>G does not affect splicing, it will result in a S3093W missense substitution. The S3093W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000373114 SCV000437114 uncertain significance Microcephalic Osteodysplastic Primordial Dwarfism 2016-06-14 criteria provided, single submitter clinical testing

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