ClinVar Miner

Submissions for variant NM_001384474.1(LOXHD1):c.4794_4795insTC (p.Ile1599fs)

gnomAD frequency: 0.00001  dbSNP: rs1598914701
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001009117 SCV001168928 likely pathogenic not provided 2018-11-15 criteria provided, single submitter clinical testing The c.4794_4795insTC variant in the LOXHD1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.4794_4795insTC variant causes a frameshift starting with codon Isoleucine 599, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 4 of the new reading frame, denoted p.Ile1599SerfsX4. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.4794_4795insTCvariant is not observed in large population cohorts (Lek et al., 2016). We interpret c.4794_4795insTC as a likely pathogenic variant.
Invitae RCV001009117 SCV002234368 pathogenic not provided 2023-10-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile1599Serfs*4) in the LOXHD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LOXHD1 are known to be pathogenic (PMID: 19732867, 21465660, 25792669). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LOXHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 817890). For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV001275167 SCV001460012 likely pathogenic Autosomal recessive nonsyndromic hearing loss 77 2020-09-16 no assertion criteria provided clinical testing

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