ClinVar Genomic variation as it relates to human health

The SLC22A5 c.34G>A; p.Gly12Ser variant (rs139203363) is reported in the literature in an individual with plasma carnitine deficiency affected with sudden infant death syndrome-like episode (Li 2010) and in two individuals who exhibited sudden unexpected death in infancy (Hertz 2016, Neubauer 2017). This variant is reported as a variant of uncertain significance in ClinVar (Variation ID: 25349).This variant is found in the general population with an overall allele frequency of 0.07% (195/280474 alleles, including one homozygote) in the Genome Aggregation Database. The glycine at codon 12 is highly conserved and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. However, this variant exhibited 51.7% of normal carnitine transport activity in functional assays, and it is unclear if this decrease is sufficient to cause disease (Frigeni 2017). Due to limited information, the clinical significance of the p.Gly12Ser variant is uncertain at this time. References: Frigeni M et al. Functional and molecular studies in primary carnitine deficiency. Hum Mutat. 2017 38:1684-1699. Hertz CL et al. Genetic investigations of sudden unexpected deaths in infancy using next-generation sequencing of 100 genes associated with cardiac diseases. Eur J Hum Genet. 2016 24:817-822. Li FY et al. Molecular spectrum of SLC22A5 (OCTN2) gene mutations detected in 143 subjects evaluated for systemic carnitine deficiency. Hum Mutat. 2010 31:E1632-1651. Neubauer J et al. Post-mortem whole-exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases. Eur J Hum Genet. 2017 25:404-409.

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 12 of the SLC22A5 protein (p.Gly12Ser). This variant is present in population databases (rs139203363, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with primary carnitine deficiency (PMID: 20574985, 28841266; 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: 25349). 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 SLC22A5 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Variant summary: SLC22A5 c.34G>A (p.Gly12Ser) results in a non-conservative amino acid change in 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 0.00084 in 1613304 control chromosomes in the gnomAD database (v4), including 3 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in SLC22A5 causing Systemic Primary Carnitine Deficiency (0.00084 vs 0.0046), allowing no strong conclusion about variant significance. c.34G>A has been reported in the literature in individuals affected with Systemic Primary Carnitine Deficiency or sudden unexpected death in infancy (e.g. Li_2010, Hertz_2016, Jacoby_2021, Barbosa-Gouveia_2021, Konig_2022). However, these data do not allow any conclusion about variant significance. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in approximately 50% of normal activity (Frigeni_2017, Koleske_2022). The following publications have been ascertained in the context of this evaluation (PMID: 34440436, 28841266, 26350513, 37510298, 34032155, 36343260, 35888728, 20574985, 34637945). ClinVar contains an entry for this variant (Variation ID: 25349). Based on the evidence outlined above, the variant was classified as uncertain significance.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. The following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with primary systemic carnitine deficiency (MIM#212140). (I) 0106 - This gene is associated with autosomal recessive disease. Nonsense and frameshift variants are typically associated with lower carnitine transport and more commonly identified in symptomatic individuals while missense variants and in-frame deletions are typically associated with residual carnitine transport activity and more commonly identified in asymptomatic individuals (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to serine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (195 heterozygotes, 1 homozygote). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and moderately conserved with a minor amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been classified as a VUS and pathogenic by multiple clinical diagnostic laboratories (ClinVar). This variant has been reported as compound heterozygous with a SLC22A5 nonsense variant in one adult female with primary carnitine deficiency and has also been identified in one individual with sudden unexpected death in infancy who was also found to carry one RYR2 and one AKAP9 variant (PMIDs: 34032155, 26350513). Additionally, it has been reported as a heterozygous VUS in a sudden infant death syndrome case and a heterozygous pathogenic variant in an individual with primary carnitine deficiency (PMIDs: 28074886, 34637945). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Mutant constructs transfected into CHO cells demonstrated 51.7% carnitine transport activity compared to WT (PMID: 28841266). (SP) 0705 - No comparable missense variants have previous evidence for pathogenicity. However, it should be noted that the p.(Gly12Asp) variant which has a higher Grantham score has been classified as a VUS in ClinVar. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

PM1 (m) PP2(sup) PM2(sup) PP3(sup) PP5(noinf)

PP3, PM3

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.