ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.189_192del (p.Phe63fs) (rs1553200990)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000595534 SCV000708173 pathogenic not provided 2017-05-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV001193268 SCV001361999 likely pathogenic Nephronophthisis 4 2019-03-05 criteria provided, single submitter clinical testing Variant summary: NPHP4 c.189_192delTGAT (p.Phe63LeufsX16) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been reported in several individuals affected with Nephronophthisis 4 in HGMD. The variant allele was found at a frequency of 4.2e-06 in 238746 control chromosomes (gnomAD). To our knowledge, no occurrence of c.189_192delTGAT in individuals affected with Nephronophthisis 4, and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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