Submissions for variant NM_003896.4(ST3GAL5):c.82+1G>C (rs878854615)

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Total submissions: 2

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000229539	SCV000288016	likely pathogenic	Salt and pepper developmental regression syndrome	2018-10-03	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 1 of the ST3GAL5 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with a ST3GAL5-related disease. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ST3GAL5 are known to be pathogenic (PMID: 15502825, 22990144, 27232954). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Illumina Clinical Services Laboratory,Illumina	RCV000229539	SCV000914945	uncertain significance	Salt and pepper developmental regression syndrome	2018-03-16	criteria provided, single submitter	clinical testing	The ST3GAL5 c.82+1G>C variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of splice donor variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance, but suspicious for pathogenicity for Amish infantile epilepsy syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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