ClinVar Miner

Submissions for variant NM_144696.6(AXDND1):c.3032-21A>T (rs775006954)

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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 RCV000517167 SCV000614352 pathogenic not provided 2016-12-13 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587601 SCV000699385 pathogenic Idiopathic nephrotic syndrome 2017-02-10 criteria provided, single submitter clinical testing Variant summary: The NPHS2 c.779T>A (p.Val260Glu) variant involves the alteration of a conserved nucleotide and results in a replacement of a medium size and hydrophobic Valine (V) with a medium size and polar Glutamine (Q) located in the Band 7 domain of the protein(InterPro). 4/4 in silico tools predict a damaging outcome for this substitution (SNPs&GO not captured due to low reliability index). This variant was found in 2/121340 control chromosomes at a frequency of 0.0000165, which does not exceed the estimated maximal expected allele frequency of a pathogenic NPHS2 variant (0.0017678). It was reported in several nephrotic syndrome patients in homozygosity indicating causality. Moreover, in at least one family, the variant co-segregated with the disease in multiple family members further supporting a pathogenic outcome. A functional study demonstrated the variant to impair localization of NPHS2 to the plasma member ant to result accumulation of the variant in ER accumulation. Taken together, this variant is classified as pathogenic.
Department of Genetics,Sultan Qaboos University Hospital, Oman RCV000761450 SCV000891536 uncertain significance Nephrotic syndrome, idiopathic, steroid-resistant 2017-12-30 criteria provided, single submitter curation

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