ClinVar Miner

Submissions for variant NM_000310.4(PPT1):c.236A>G (p.Asp79Gly)

dbSNP: rs137852697
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001571117 SCV001795533 pathogenic not provided 2021-07-01 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect as palmitoyl-CoA hydrolase activity is reduced by ~90% as compared to wild type (Bellizzi et al., 2000); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 9425237, 10781062, 27535533, 21228398, 9664077, 11440996, 29576218)
Labcorp Genetics (formerly Invitae), Labcorp RCV000009452 SCV004291785 likely pathogenic Neuronal ceroid lipofuscinosis 1 2023-08-14 criteria provided, single submitter clinical testing 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. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (PMID: 9425237). Experimental studies have shown that this missense change affects PPT1 function (PMID: 10191107, 11440996). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 8901). This missense change has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 9425237). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs137852697, gnomAD 0.0009%). This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 79 of the PPT1 protein (p.Asp79Gly).
OMIM RCV000009452 SCV000029670 pathogenic Neuronal ceroid lipofuscinosis 1 1998-02-01 no assertion criteria provided literature only

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