ClinVar Miner

Submissions for variant NM_001384474.1(LOXHD1):c.5224C>T (p.Arg1742Cys)

gnomAD frequency: 0.00004  dbSNP: rs561122654
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002307715 SCV002600610 uncertain significance not specified 2022-10-20 criteria provided, single submitter clinical testing Variant summary: LOXHD1 c.5085+957C>T (NM_144612.6) is located at a position not widely known to affect splicing. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 3.2e-05 in 156418 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. The variant causes an amino acid change in the shorter transcript NM_001145472.3 (c.1891C>T, p.Arg631Cys). c.1891C>T has been reported in the literature in an individual affected with Nonsyndromic Hearing Loss (Yu_2021). However, this report does not provide unequivocal conclusions about association of the variant with Nonsyndromic Hearing Loss And Deafness, Type 77. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.
Invitae RCV002537624 SCV003455331 likely benign not provided 2022-08-09 criteria provided, single submitter clinical testing
Center for Molecular Medicine, Children’s Hospital of Fudan University RCV001261863 SCV001439202 likely pathogenic Autosomal recessive nonsyndromic hearing loss 77 2020-09-30 no assertion criteria provided clinical testing

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