ClinVar Miner

Submissions for variant NM_144696.6(AXDND1):c.3032-1887G>A (rs780761368)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000681863 SCV000842935 pathogenic not provided 2019-05-31 criteria provided, single submitter clinical testing The best available variant frequency is uninformative because there are too few occurrences in population data. Statistically enriched in patients compared to ethnically matched controls. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Located in potentially critical domain of the protein. Occurs in three or more cases with a recessive pathogenic variant in the same gene.
Integrated Genetics/Laboratory Corporation of America RCV000781678 SCV000919906 likely pathogenic Idiopathic nephrotic syndrome 2018-10-01 criteria provided, single submitter clinical testing Variant summary: NPHS2 c.851C>T (p.Ala284Val) results in a non-conservative amino acid change located in the Band 7 domain of 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 4.1e-06 in 244704 control chromosomes (gnomAD). The variant, c.851C>T, has been reported in the literature in multiple individuals affected with Nephrotic Syndrome, Type 2, either in compound heterozygosity with the well-reported risk variant p.R229Q including at-least one homozygote (Tsukaguchi_2002, Santin_2011, Karle_2002). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Gharavi Laboratory,Columbia University RCV000681863 SCV000809342 pathogenic not provided 2018-09-16 no assertion criteria provided research

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