ClinVar Genomic variation as it relates to human health

ACMG classification criteria: PS3 supporting, PS4 strong, PM2 supporting

Reported multiple times in the heterozygous state in possible association with atypical hemolytic-uremic syndrome, however, detailed clinical and segregation information was not provided in all instances (PMID: 22669319, 25899302, 30046676, 34169201, 33841858); Published functional studies demonstrate that this alteration leads to decreased binding of C3b to CFH in vitro and modest but significant decreases in factor F and membrane cofactor protein association rate and binding affinity compared to wild type (PMID: 22669319, 25608561); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22669319, 36631797, 37744338, 25608561, 24736606, 31589614, 30046676, 33609329, 25899302, 34169201, 33841858, 37567446, 35385571, 32765494, 29888403, 24799305, 23852337, 28025630, 24853370, 25188723, 24038559, 30225264, 34631043)

This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 65 of the C3 protein (p.Lys65Gln). This variant is present in population databases (rs539992721, gnomAD 0.009%). This missense change has been observed in individuals with atypical hemolytic uremic syndrome (PMID: 22669319, 25608561, 30046676, 33609329, 35372954). This variant is also known as K43Q. ClinVar contains an entry for this variant (Variation ID: 381739). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt C3 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects C3 function (PMID: 22669319, 25608561). 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.

Variant summary: C3 c.193A>C (p.Lys65Gln) results in a conservative amino acid change located in the MG2 domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 251474 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in C3 causing C3 Deficiency (4.8e-05 vs 0.0011), allowing no conclusion about variant significance. c.193A>C has been reported in the literature in multiple heterozygous individuals affected with atypical Haemolytic uraemic syndrome without strong evidence of segregation (examples: Volokhina_2012, Duvvari_2014, Fidalgo_2017, Wilson_2020, Akesson_2021, Ardissino_2021). These report(s) do not provide unequivocal conclusions about association of the variant with C3 Deficiency. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Volokhina_2012). The following publications have been ascertained in the context of this evaluation (PMID: 22669319, 24736606, 30046676, 35372954, 33609329, : 34169201). ClinVar contains an entry for this variant (Variation ID: 381739). Based on the evidence outlined above, the variant was classified as uncertain significance.

C3 p.Lys65Gln (c.193A>C) is a missense variant that changes the amino acid at residue 65 from Lysine to Glutamine. This variant has been observed in at least one proband affected with a C3-related disorder (PMID:22669319;28941939;33841858;33609329;30659006). Functional studies have been reported; however, the significance of the findings remain unclear (PMID:22669319;25608561). It is absent or not present at a significant frequency in gnomAD. In silico models agree that this variant is possibly or probably damaging. In conclusion, we classify C3 p.Lys65Gln (c.193A>C) as a variant of unknown significance.

This variant is classified as Risk allele. Evidence in support of pathogenic classification: Variant is present in gnomAD <0.01 (v4: 237 heterozygote(s), 0 homozygote(s)); This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic/pathogenic and as a VUS by clinical laboratories in ClinVar, and identified in the literature in individuals with atypical haemolytic-uraemic syndrome (PMIDs: 22669319, 32765494, 37744338); This variant has moderate functional evidence supporting abnormal protein function. In vitro analysis using an ELISA assay has shown this variant results in a significant decrease in complement factor H binding compared to wildtype (PMID: 22669319). Additional information: Variant is predicted to result in a missense amino acid change from lysine to glutamine; This variant is heterozygous; This gene is associated with both recessive and dominant disease. Missense variants with a gain of function or possible loss of function disease mechanism have been reported in a heterozygous state in individuals with atypical haemolytic-uraemic syndrome and/or age-related macular degeneration, whereas heterozygous null variants have been rarely reported in individuals with atypical haemolytic-uraemic syndrome (PMID: 18796626, 29888403). Individuals with biallelic null variants have C3 deficiency (PMID: 21501302); Alternative amino acid change(s) at the same position are present in gnomAD (highest allele count: v4: 1 heterozygote(s), 0 homozygote(s)); Variant is located in the annotated macroglobulin domain (DECIPHER); Missense variant with inconclusive in silico prediction and uninformative conservation; Loss of function and gain of function are known mechanisms of disease in this gene and are associated with C3 deficiency (MIM#613779), susceptibility to atypical hemolytic uraemic syndrome 5 (MIM#612925), and age-related macular degeneration 9 (MIM#611378) (PMID: 27814381, 18796626); The condition associated with this gene has incomplete penetrance. Heterozygous variants causing atypical haemolytic-uraemic syndrome are commonly inherited from healthy parents (PMID: 18796626); Inheritance information for this variant is not currently available in this individual.

PP3, PS3, PS4

This patient is heterozygous for a known pathogenic variant, c.193A>C (p.Lys65Gln), in the C3 gene. This variant (dbSNP: rs539992721) has been reported in the Exome Aggregation Consortium (ExAC) database (http://exac.broadinstitute.org/) with a very low allele frequency of 0.006% (7/121402 alleles). This variant is reported in the C3 aHUS mutation database (www.fh-hus.org/) including three atypical haemolytic uremic syndrome (aHUS) patients whom acquired the illness as an adult, with first aHUS episode after renal transplantation or suffered recurrence of the disease after renal transplantation (Volokhina et al 2012 Pediatr Nephrol 27:1519-1524). The authors also performed functional studies which showed the C3 mutant protein decreases C3b binding to CFH in vitro.