ClinVar Miner

Submissions for variant NM_144612.6(LOXHD1):c.5023C>T (p.Arg1675Cys) (rs201060702)

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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 RCV000155143 SCV000204829 likely benign not specified 2017-08-03 criteria provided, single submitter clinical testing p.Arg1675Cys in exon 32 of LOXHD1: This variant is not expected to have clinical significance due to a lack of conservation across species including mammals. Of note, more than 40 mammalian species have a cysteine (Cys) at this position des pite high nearby amino acid conservation. In addition, computational analyses do not suggest a high likelihood of impact to the protein. This variant has been i dentified in 0.13% (252/182290) of all chromosomes including 2 homozygotes with the highest frequencies in 0.44% (109/24794) of Latino chromosomes and 0.42% (36 /8536) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (gnomA D, http://gnomad.broadinstitute.org; dbSNP rs201060702).
GeneDx RCV000827980 SCV000969654 likely benign not provided 2018-05-21 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.
Invitae RCV000827980 SCV001109738 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001124015 SCV001282919 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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