ClinVar Genomic variation as it relates to human health

Variant summary: COL4A4 c.81_86delACTCAT (p.Ile29_Leu30del) results in an in-frame deletion that is predicted to remove two amino acids from exon 3 of the encoded protein. The variant allele was found at a frequency of 4.8e-05 in 249154 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in COL4A4 causing Alport Syndrome, Autosomal Recessive (4.8e-05 vs 0.0016), allowing no conclusion about variant significance. c.81_86delACTCAT has been reported in the literature in multiple compound heterozygous individuals affected with Alport Syndrome, including at least one case where it has been confirmed to be in trans with a pathogenic variant (e.g. Storey_2013, Moriniere_2014, Mallett_2017, Zhang_2021). These data indicate that the variant is very likely to be associated with disease. c.81_86delACTCAT has also been found in the heterozygous state in two individuals with thin basement membrane nephropathy (Weber_2016, Mallett_2017). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five assessments for this variant have been submitted to ClinVar after 2014 with conflicting assessments (likely pathogenic n=2, VUS n=3). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This sequence change is an inframe deletion of 6 bp predicted to cause the deletion of isoleucine and leucine at positions 29 and 30 of the COL4A4 protein (p.Ile29_Leu30del). The region deleted is moderately conserved (100 vertebrates, UCSC), and is located in a non-repeat region within the signal peptide. The variant is present in a large population cohort at a frequency of 0.005%, consistent with recessive disease (rs771943519, 14/280,560 alleles, 0 homozygotes in gnomAD v2.1.1 - PM2). It has been reported in at least four Alport syndrome cases with a second pathogenic COL4A4 allele (PMID: 24052634, 24854265, 28844315 - PM3_Strong), and heterozygous in at least two probands with a clinical diagnosis of thin basement membrane nephropathy (PMID: 26809805, 28844315). Based on the classification scheme RMH ACMG Guidelines v1.1.1, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PM3_Strong, PM2.

The c.81_86delACTCAT (p.I29_L30del) alteration, located in exon 3 (coding exon 2) of the COL4A4 gene, results from an in-frame deletion of 6 nucleotides at positions 81 to 86. This results in the deletion of 2 amino acids between codons 29 and 30. Based on data from gnomAD, the c.81_86delACTCAT allele has an overall frequency of 0.005% (14/280560) total alleles studied. The highest observed frequency was 0.012% (3/24180) of African alleles. This variant has been reported in conjunction with a second COL4A4 variant in individuals with Alport syndrome and hematuric nephropathy (Storey, 2013; Morinière, 2014; Pinto E Vairo, 2021; Zhang, 2021); however, phase of the variants was not confirmed in most individuals. This variant was also detected with no second COL4A4 variant in individuals with hematuria and hematuric nephropathy (Morinière, 2014; Weber, 2016; Alge, 2023). Based on the available evidence, this alteration is classified as likely pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function is a known mechanism of disease for this gene and is associated with COL4A4-related nephropathy. Dominant negative is a suspected mechanism of disease for this gene as it is a structural protein (PMIDs: 12028435, 24046192). (I) 0108 - This gene is associated with both recessive and dominant disease. Alport syndrome typically has biallelic inheritance, although rare cases of monoallelic inheritance have been reported (PMID: 28704582). TBMN and focal segmental glomerulosclerosis (FSGS) are associated with autosomal dominant inheritance (OMIM, PMIDs: 16467446, 17942953). (I) 0216 - In-frame deletion in a non-repetitive region that has low conservation. (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD v2 <0.01 for a condition (14 heterozygotes, 0 homozygotes). (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been observed in over ten individuals with COL4A4-related nephropathy, and has been associated with both AR and AD forms of disease (ClinVar, LOVD, PMIDs: 28844315, 24854265, 26809805, 24052634, 33772369). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1102 - Strong phenotype match for this individual. (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-frame deletion of two amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24052634, 35759000, 28632965, 34758253, 36938085, 37248651, Kim2021[case report], 34746741, 28844315, 26809805, 33772369)

PM2, PM3_strong, PM4, PS4

This variant, c.81_86del, results in the deletion of 2 amino acid(s) of the COL4A4 protein (p.Ile29_Leu30del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs771943519, gnomAD 0.01%). This variant has been observed in individuals with autosomal dominant and recessive Alport syndrome and/or thin basement membrane nephropathy and hematuria (PMID: 24052634, 24854265, 26809805, 28632965, 28844315; internal data). This variant is also known as p.Ile27_Ile29delinsIle. ClinVar contains an entry for this variant (Variation ID: 369962). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.005%). Predicted Consequence/Location: Inframe deletion located in a nonrepeat region: predicted to change the length of the protein and disrupt normal protein function. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000369962 /PMID: 24052634). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

This patient is heterozygous for a known variant, c.81_86del (p.Ile29_Leu30del), in the COL4A4 gene. This variant results in the in-frame deletion of two residues p.Ile29 and p.Leu30, and has been previously reported in trans with another COL4A4 pathogenic variant in two patients with Alport syndrome (Storey et al 2013 J Am Soc Nephrol 24:1945-54). Storey et al considered this variant to be pathogenic.

This patient is heterozygous for a known variant, c.81_86del (p.Ile29_Leu30del), in the COL4A4 gene. This variant results in the in-frame deletion of two residues p.Ile29 and p.Leu30, and has been previously reported in trans with another COL4A4 pathogenic variant in two patients with Alport syndrome (Storey et al 2013 J Am Soc Nephrol 24:1945-54). Storey et al considered this variant to be pathogenic.