ClinVar Miner

Submissions for variant NM_002861.5(PCYT2):c.866C>T (p.Pro289Leu)

gnomAD frequency: 0.00002  dbSNP: rs1204173741
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001235496 SCV001408185 uncertain significance not provided 2020-03-10 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been observed in individual(s) with complex hereditary spastic paraplegia (PMID: 31637422). This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with leucine at codon 307 of the PCYT2 protein (p.Pro307Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine.
OMIM RCV001003406 SCV001161693 pathogenic Spastic paraplegia 82, autosomal recessive 2020-02-14 no assertion criteria provided literature only

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