ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.774del (p.Phe258fs) (rs780267761)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000414560 SCV000491465 pathogenic not provided 2016-03-06 criteria provided, single submitter clinical testing The c.774delT variant in the LZTR1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.774delT variant causes a frameshift starting with codon Phenylalanine 258, changes this amino acid to a Leucine residue, and creates a premature Stop codon at position 93 of the new reading frame, denoted p.Phe258LeufsX93. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.774delT variant was not observed with any significant frequency in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.774delT as a pathogenic variant.
Invitae RCV000414560 SCV001404178 pathogenic not provided 2020-10-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Phe258Leufs*93) in the LZTR1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs780267761, ExAC 0.002%). This variant has not been reported in the literature in individuals with LZTR1-related conditions. ClinVar contains an entry for this variant (Variation ID: 372924). Loss-of-function variants in LZTR1 are known to be pathogenic (PMID: 24362817, 25335493, 25480913, 29469822, 30442762, 30859559). For these reasons, this variant has been classified as Pathogenic.
University of Washington Center for Mendelian Genomics, University of Washington RCV001291506 SCV001480011 association Autism spectrum disorder no assertion criteria provided research

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