ClinVar Genomic variation as it relates to human health

Variant classified as Uncertain Significance - Favor Benign. The p.Thr196Ile var iant in SPRED1 has been reported in 2 individuals with multiple cafe-au-lait mac ules (CALMs), with or without freckling, who were negative for deleterious NF1 v ariants (Messiaen 2009, Spencer 2011). This variant has also been identified in 11/65518 European chromosomes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs147474792). In vitro functional studies suggest that the p.Thr196Ile variant may not impact protein function; however, these ty pes of assays may not accurately represent biological function (Messiaen 2009). Additional computational prediction tools and conservation analysis suggest that this variant may not impact the protein, though this information is not predict ive enough to rule out pathogenicity. In summary, while the clinical significanc e of the p.Thr196Ile variant is uncertain, these data suggest that it is more li kely to be benign.

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

In silico analysis supports that this missense variant does not alter protein structure/function; Published functional studies demonstrate ERK activation and cell differentiation levels comparable to wildtype (Messiaen et al., 2019); Identified in individuals with multiple cafe-au-lait macules or other features suspicious for Neurofibromatosis-Noonan syndrome (Messiaen et al., 2009; Witkowski et al., 2020); This variant is associated with the following publications: (PMID: 22753041, 32107864, 19920235, 21548021)

Variant summary: SPRED1 c.587C>T (p.Thr196Ile) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00011 in 250856 control chromosomes, predominantly at a frequency of 0.0002 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 35 fold of the estimated maximal expected allele frequency for a pathogenic variant in SPRED1 causing Neurofibromatosis Type 1-Like Syndrome (Legius Syndrome) phenotype (5.6e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.587C>T has been reported in the literature in an individual receiving RASopathy panel testing and in a male individual with craniofacial dysmorphisms, ocular abnormalities, heart defects and cryptorchidism, without strong evidence for causality (Papadopoulos_2022, Witkowski_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Neurofibromatosis Type 1-Like Syndrome (Legius Syndrome). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 35904599, 32107864). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 196 of the SPRED1 protein (p.Thr196Ile). This variant is present in population databases (rs147474792, gnomAD 0.02%). This missense change has been observed in individual(s) with café-au-lait macules, neurofibromatosis type 1-like syndrome, and/or Noonan-like dysmorphic features (PMID: 19920235, 21548021, 35904599). ClinVar contains an entry for this variant (Variation ID: 229269). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is not expected to disrupt SPRED1 function with a negative predictive value of 95%. Experimental studies have shown that this missense change does not substantially affect SPRED1 function (PMID: 19920235). 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.

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.