ClinVar Miner

Submissions for variant NM_001089.3(ABCA3):c.3600CTT[3] (p.Phe1203del)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Johns Hopkins Genomics, Johns Hopkins University RCV001250543 SCV001425356 likely pathogenic Surfactant metabolism dysfunction, pulmonary, 3 2020-03-19 criteria provided, single submitter clinical testing This previously reported ABCA3 variant (rs750862009) is rare in a large population dataset (gnomAD: 21/282206 total alleles; 0.007441%; no homozygotes). This single amino acid deletion has been seen multiple times in patients with a phenotype consistent with ABCA3-related surfactant deficiency who also carry a second pathogenic ABCA3 variant on the opposite allele. We consider this variant to be likely pathogenic.
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV001250543 SCV001443747 likely pathogenic Surfactant metabolism dysfunction, pulmonary, 3 2020-02-12 criteria provided, single submitter clinical testing This variant has been previously reported as a compound heterozygous change in multiple patients with interstitial lung disease, including chronic pneumonitis, pneumonia, pulmonary fibrosis and emphysema (PMID: 16641205, 18024538, 24871971, 26780485). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.0074% (21/282206) and thus is presumed to be rare. Based on the available evidence, the c.3609_3611del (p.Phe1203del) variant is classified as Likely Pathogenic.

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