ClinVar Miner

Submissions for variant NM_144612.6(LOXHD1):c.1708G>A (p.Asp570Asn) (rs140437150)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041191 SCV000064882 benign not specified 2017-12-21 criteria provided, single submitter clinical testing p.Asp570Asn variant in exon 13 of LOXHD1: This variant is not expected to have c linical significance because it has been identified in 193/16434 (1.2%) African American chromosomes by the genome Aggregation Database (gnomAD, http://gnomad.b roadinstitute.org/; dbSNP rs140437150). ACMG/AMP criteria applied: BA1.
GeneDx RCV000041191 SCV000618523 uncertain significance not specified 2017-06-22 criteria provided, single submitter clinical testing The D570N variant in the LOXHD1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The D570N variant is observed in 26/2,772 (0.94%) alleles from individuals of African background, with no homozygous control individuals reported, in the ExAC dataset (Lek et al., 2016). The D570N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret D570N as a variant of uncertain significance.
Invitae RCV000887253 SCV001030802 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001123332 SCV001282163 uncertain significance Deafness, autosomal recessive 77 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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