ClinVar Miner

Submissions for variant NM_000310.4(PPT1):c.272A>C (p.Gln91Pro)

gnomAD frequency: 0.00001  dbSNP: rs386833639
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049598 SCV000800701 uncertain significance Neuronal ceroid lipofuscinosis 1 2018-04-25 criteria provided, single submitter clinical testing
Invitae RCV000049598 SCV001415148 pathogenic Neuronal ceroid lipofuscinosis 1 2024-01-29 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 91 of the PPT1 protein (p.Gln91Pro). This variant is present in population databases (rs386833639, gnomAD 0.02%). This missense change has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 17044973; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56187). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PPT1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049598 SCV000082005 probable-pathogenic Neuronal ceroid lipofuscinosis 1 no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Natera, Inc. RCV000049598 SCV002086004 uncertain significance Neuronal ceroid lipofuscinosis 1 2020-04-17 no assertion criteria provided clinical testing

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