The S100F variant in the CTSD gene has been reported previously in an individual with congenital neuronal lipofuscinosis who was homozygous for the S100F variant (Fritchie et al., 2009). Functional studies of the S100F variant demonstrated a damaging effect with severely reduced cathepsin D enzyme activity (Fritchie et al., 2009). The S100F variant is not observed in large population cohorts (Lek et al., 2016). The S100F variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret S100F as a likely pathogenic variant.

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 100 of the CTSD protein (p.Ser100Phe). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with congenital neuronal ceroid lipofuscinosis (PMID: 18762956). ClinVar contains an entry for this variant (Variation ID: 205363). 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 CTSD protein function. Experimental studies have shown that this missense change affects CTSD function (PMID: 18762956). 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.

The p.S100F variant (also known as c.299C>T), located in coding exon 3 of the CTSD gene, results from a C to T substitution at nucleotide position 299. The serine at codon 100 is replaced by phenylalanine, an amino acid with highly dissimilar properties. This alteration was detected in the homozygous state in an individual with congenital neuronal ceroid lipofuscinosis (NCL). In addition, authors found very low enzyme activity in this individual's fibroblasts as well as reduced CTSD activity in functional studies (Fritchie K et al. Acta Neuropathol., 2009 Feb;117:201-8). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Variant summary: CTSD c.299C>T (p.Ser100Phe) results in a non-conservative amino acid change located in the Peptidase family A1 domain (IPR033121) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 250438 control chromosomes (gnomAD). c.299C>T has been reported in the literature in an individual affected with Neuronal Ceroid-Lipofuscinosis (Batten Disease; Fritchie_2009). These data indicate that the variant may be associated with disease. Publications report experimental evidence evaluating an impact on protein function, finding profound reductions in enzymatic activity (Fritchie_2009, Bunk_2021). The following publications have been ascertained in the context of this evaluation (PMID: 18762956, 33681191). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.