ClinVar Miner

Submissions for variant NM_001042432.2(CLN3):c.782C>T (p.Ser261Leu)

gnomAD frequency: 0.00001  dbSNP: rs199627744
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001042505 SCV001206188 uncertain significance Neuronal ceroid lipofuscinosis 2022-08-31 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 261 of the CLN3 protein (p.Ser261Leu). This variant is present in population databases (rs199627744, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CLN3-related conditions. ClinVar contains an entry for this variant (Variation ID: 840500). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
GeneDx RCV001732023 SCV001981991 uncertain significance not provided 2021-04-02 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV001785772 SCV002027105 uncertain significance Neuronal ceroid lipofuscinosis 3 2021-09-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV002553086 SCV003651789 uncertain significance Inborn genetic diseases 2022-09-29 criteria provided, single submitter clinical testing The c.782C>T (p.S261L) alteration is located in exon 10 (coding exon 9) of the CLN3 gene. This alteration results from a C to T substitution at nucleotide position 782, causing the serine (S) at amino acid position 261 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001042505 SCV001452334 uncertain significance Neuronal ceroid lipofuscinosis 2020-09-16 no assertion criteria provided clinical testing

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