ClinVar Genomic variation as it relates to human health

The ABCA3 c.838C>T (p.Arg280Cys) missense variant has been reported three studies in which it is found in three patients in a compound heterozygous state including in one child with interstitial lung disease secondary to ABCA3 deficiency in a compound heterozygous state with a second missense variant, in one infant with unexplained respiratory distress, in whom a second variant could not be identified and in a third patient with pulmonary surfactant deficiency, in cis with a stop-gained variant and in trans with a synonymous variant (Somaschini et al. 2007; Williamson et al. 2014; Jackson et al. 2015). Control data are unavailable for this variant, which is reported at a frequency of 0.00024 in the European (non-Finnish) population of the Exome Aggregation Consortium. Weichert et al. (2011) demonstrated that human alveolar epithelial A549 cells expressing the p.Arg280Cys variant partially impaired transport of the ABCA3 protein through the endoplasmic reticulum (ER) leading to retention in the ER compared to wild type. Based on the evidence, the p.Arg280Cys variant is classified likely pathogenic for pulmonary surfactant metabolism dysfunction. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This variant has been identified in multiple individuals with clinical features associated with this gene (PMID: 25712598, 24115460, 17517255, 22337229). Assessment of experimental evidence suggests this variant results in abnormal protein function (PMID: 21214890). The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study.

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 280 of the ABCA3 protein (p.Arg280Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individuals with autosomal recessive interstitial lung disease (PMID: 17517255, 24115460, 24871971, 32238781). ClinVar contains an entry for this variant (Variation ID: 318566). 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 ABCA3 protein function. Experimental studies have shown that this missense change affects ABCA3 function (PMID: 21214890). 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.

The p.R280C variant (also known as c.838C>T), located in coding exon 5 of the ABCA3 gene, results from a C to T substitution at nucleotide position 838. The arginine at codon 280 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration was first reported in an infant with neonatal respiratory distress who passed away at 2 days of age; a second alteration was not identified (Somaschini M et al. J. Pediatr. 2007; 150:649-53, 653.e1). This alteration was identified in conjunction with p.E690G in an individual with respiratory distress; however, information on the phase (cis/trans) of the two alterations was not provided (Williamson M and Wallis C Pediatr. Pulmonol. 2014; 49:299-301). A report of a female neonate with respiratory distress and radiological confirmation of surfactant deficiency also detected this alteration in cis with a nonsense pathogenic mutation along with another mutation in trans (Jackson T etl al. J Perinat. 2015;35:231-232). In our own internal cohort, this alteration was also detected in cis with a nonsense mutation in one patient. Functional studies showed this mutation can lead to partial retention of the ABCA3 protein in the endoplasmic reticulum (ER) and induce apoptosis of lung epithelial cells (Weichert N et al. Respir. Res. 2011; 12:4). Based on the available evidence to date, this variant is likely to be pathogenic.

Variant summary: ABCA3 c.838C>T (p.Arg280Cys) 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 0.00017 in 250570 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in ABCA3 causing Pulmonary surfactant metabolism dysfunction (0.00017 vs 0.0011), allowing no conclusion about variant significance. c.838C>T has been reported in the literature in individuals affected with Pulmonary surfactant metabolism dysfunction (Somaschini_2007, Turcu_2013, Jackson_2015). These reports do not provide unequivocal conclusions about association of the variant with Pulmonary surfactant metabolism dysfunction. Co-occurrences with a pathogenic variant has been reported (ABCA3 c.4765C>T, p.Q1589X), providing supporting evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in partial disruption of normal activity. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (Pathogenic/likely pathogenic, n=3, VUS n=3). Based on the evidence outlined above, the variant was classified as uncertain significance.

The p.Arg280Cys variant in ABCA3 has been reported in the compound heterozygous state in 1 individual with interstitial lung disease (ILD) and has also been rep orted in cis with the p.Q1589X variant in ABCA3 in 2 individuals with ILD who c arried another variant in trans (Williamson 2014, Wambach 2014, Jackson 2015). I n vitro functional studies provide some evidence that the p.Arg280Cys variant ma y impact protein function (Weichert 2011). However, these types of assays may no t accurately represent biological function. This variant has been reported in Cl inVar (Variation ID: 318566) and has been identified in 30/111616 European chrom osomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute. org/; dbSNP rs201299260). Computational prediction tools and conservation analys is suggest that the p.Arg280Cys variant may impact the protein, though this info rmation is not predictive enough to determine pathogenicity. In summary, the cli nical significance of the p.Arg280Cys variant is uncertain. ACMG/AMP Criteria ap plied: PP3, PS3_Supporting, PM3_Supporting, BP2.

This ABCA3 variant (rs201299260) is rare (<0.1%) in a large population dataset (gnomAD: 45/281924 total alleles; 0.016%; no homozygotes). Two submitters in ClinVar classify c.838C>T as a variant of uncertain clinical significance. This variant has been reported in numerous patients with respiratory distress. A functional study has demonstrated that this variant affects normal ABCA3 protein trafficking and folding. This variant is considered pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with surfactant metabolism dysfunction, pulmonary, 3 (MIM#610921). (I) 0106 - This gene is associated with autosomal recessive disease. (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 (v2) <0.01 for a recessive condition (45 heterozygotes, 0 homozygotes). (SP) 0309 - Multiple alternative amino acid changes at the same position has been observed in gnomAD (v2 & v3) (highest allele count: 231 heterozygotes, 1 homozygote). (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 ABC-2 family transporter protein domain (DECIPHER) (I) 0708 - Another missense variant comparable to the one identified in this case has conflicting previous evidence for pathogenicity. p.(Arg280His) has been classified as a VUS by multiple clinical laboratories in ClinVar, and as likely benign by one. This variant has also been observed as heterozygous in an individual with idiopathic interstitial pneumonia, and with a second ABCA3 variant in an individual with lung disease (phase unknown) (PMIDs: 20656946, 27516224). (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been classified as pathogenic, likely pathogenic and as a VUS by clinical laboratories in ClinVar. This variant has been observed in two individuals with interstitial lung disease who also had a second ABCA3 variant (one compound heterozygous, the other phase unknown) (PMIDs: 23625987, 24115460, 36370864). However, this variant has also been observed in cis with a nonsense variant p.(Gln1589*) in three individuals with respiratory failure, once as a homozygous allele, once in trans with another ABCA3 missense variant, and once as heterozygous (PMIDs: 25712598, 24871971). (I) 1002 - This variant has moderate functional evidence supporting abnormal protein function. This variant has been shown to be partially retained in the endoplasmic reticulum, leading to ER stress and apoptosis (PMID: 21214890). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign