ClinVar Miner

Submissions for variant NM_144612.6(LOXHD1):c.2916_2924AGAGGAGGA[1] (p.Glu976_Glu978del) (rs765944082)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000603237 SCV000712199 uncertain significance not specified 2017-09-22 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Benign. The p.Glu976_Glu978 del variant in LOXHD1 has now been identified by our laboratory in the heterozyg ous state in 2 individuals with hearing loss, neither of whom had a variant affe cting the other copy of the LOXHD1 gene. This variant is located within a polygl utamic acid tract that consists of 8 glutamic acid (Glu) residues in the human r eference genome, and results in an in-frame deletion of 3 glutamic acids (Glu) r esidues. This variant has been identified in 7/73148 European chromosomes and a similar variant resulting the same amino acid change has been identified in 48/2 2822 (0.2%) of South Asian chromosomes including 1 homozygote by the Genome Aggr egation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs765944082 an d rs753461629). The variant is not predicted to alter the reading frame of the p rotein and the polyglutamic acid tract region where the variant occurs is poorly conserved across species, suggesting that the variant may be tolerated; however , this information is not sufficient to rule out pathogenicity. In summary, whil e the clinical significance of the p.Glu976_Glu978del variant is uncertain, avai lable data suggest that it is more likely to be benign.
GeneDx RCV000827579 SCV000969232 likely benign not provided 2018-06-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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