ClinVar Genomic variation as it relates to human health

This heterozygous missense variant in the COL4A3 gene (autosomal recessive transmission) is present in a male patient with Alport syndrome who also harbours a non-sense variant in the same gene (see below). The segregation analysis could not be done, but regarding the clinical presentation of the patient, it is assumed that these two variants are present in compound heterozygosity

Variant summary: COL4A3 c.4981C>T (p.Arg1661Cys) 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 0.00036 in 249438 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not higher than expected for a pathogenic variant in COL4A3 causing Autosomal Recessive Alport Syndrome (0.0019), allowing no conclusion about variant significance. The c.4981C>T has been reported in the literature in at least three individuals affected with Autosomal Recessive Alport Syndrome with other (likely) pathogenic COL4A3 variants in trans (Storey_2013, ClinVar: SCV000537703.1). In addition, the variant was also reported in several individuals affected with Alport syndrome where the other variant in trans was not specified (e.g. Heidet_2001, Weber_2016, Savige_2016). These data indicate that the variant is likely associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 11 submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic (n=2) / likely pathogenic (n=6) or VUS (n=3). Based on the evidence outlined above, the variant was classified as likely pathogenic.

The c.4981C>T;p.(Arg1661Cys) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 287915; PMID: 26809805; PMID: 25229338); PMID: 25229338; PMID: 24052634; PMID: 24052634 - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (C4) - PM1. The p.(Arg1661Cys) was detected in trans with a pathogenic variant (PMID: 26809805; PMID: 24052634; PMID: 24052634) - PM3. The variant co-segregated with disease in multiple affected family members (PMID: 26809805; 25229338) - PP1_strong. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3.and allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is pathogenic.

The COL4A3 c.4981C>T variant is predicted to result in the amino acid substitution p.Arg1661Cys. The p.Arg1661 residue lies in the non-collagenous domain. This variant has been reported to be pathogenic for autosomal recessive Alport syndrome when in the presence with another pathogenic variant (Heidet et al. 2001. PubMed ID: 11134255; Storey et al. 2013. PubMed ID: 24052634). This variant in the heterozygous status was also reported in one family with focal segmental glomerulosclerosis (FSGS) (Malone et al. 2014. PubMed ID: 25229338). This variant in the compound heterozygous condition along with another COL4A3 missense variant has been reported in a patient with autosomal recessive focal segmental glomerulosclerosis (FSGS) (Braunisch et al. 2018. PubMed ID: 29946535). This variant is reported in 0.058% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-228176554-C-T). This variant is interpreted as pathogenic.

PP3, PM2_supporting, PM3_very_strong

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1661 of the COL4A3 protein (p.Arg1661Cys). This variant is present in population databases (rs201697532, gnomAD 0.06%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with Alport syndrome (PMID: 11134255, 24052634, 26809805; 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: 287915). 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 COL4A3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

This variant is interpreted as likely pathogenic for Alport syndrome spectrum, autosomal recessive. The following ACMG Tag(s) were applied: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (PP3_moderate; REVEL score 0.918). For recessive disorders, detected in trans with a pathogenic variant (PM3_strong; PMID: 24052634, 37362409, 38214412).

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with Alport syndrome, MONDO:0018965, COL4A3-related. Glycine changes that are part of a G-X-Y repeat in the triple helix of a collagen domain are known to have a dominant negative effect (PMID: 12028435). (I) 0108 - This gene is associated with both recessive and dominant disease, Alport syndrome 3B (MIM#620536) and Alport syndrome 3A (MIM#104200), respectively (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 99 heterozygotes, 1 homozygote). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (9 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated C4 domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic/pathogenic by multiple clinical laboratories in ClinVar; it has also been classified as a VUS. This variant has been reported in several compound heterozygous individuals with Alport syndrome (PMIDs: 24052634, 29946535, 37362409). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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: 30406062, 30487145, 30773290, 25229338, 20847057, 33774617, 32939031, 36013122, 32359821, 11134255, 34746741, 34313030, 30586318, 33532864, 37163122, 27485810, Bailo[CaseReport]2021, 26809805, 24052634, 29946535)

This individual is also heterozygous for the c.4981C>T variant in the COL4A3 gene, which results in the amino acid substitution of arginine to cysteine at residue 1661, p.(Arg1661Cys). This variant has been reported in the gnomAD v4.1.1 browser (http://gnomad.broadinstitute.org accessed: 24/07/2024) with aN allele frequency of 0.05% (953 out of 1613914 alleles, including 3 homozygous individuals). The allele frequency of this variant is too high for this variant to cause fully penetrant autosomal dominant COL4A3 related disorders. However, it has been widely reported in multiple unrelated individuals with autosomal recessive COL4A3 related disorders. In such cases, the c.4981C>T p.(Arg1661Cys) was found in compound heterozygosity with another COL4A3 disease causing variant (Braunisch et al 2018 PMID: 29946535; Weber et al 2016 PMID: 26809805; Storey et al 2013 PMID: 24052634). This variant alters a highly conserved arginine in the NCI domain of COL4A3 (LeBleu et al 2010 PMID: 20847057). In silico analysis of pathogenicity (through Alamut Visual v2.13) using PolyPhen2, SIFT and MutationTaster all suggest that this variant is likely to be pathogenic. This variant is considered to be pathogenic according to the ACMG guidelines (Evidence used: PM3_Very strong, PM1, PM2_Supporting, PP3_Moderate). .