ClinVar Miner

Submissions for variant NM_144612.6(LOXHD1):c.4217C>T (p.Ala1406Val) (rs146739496)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000155145 SCV000204831 benign not specified 2015-01-20 criteria provided, single submitter clinical testing p.Ala1406Val in exon 28 LOXHD1: This variant is not expected to have clinical si gnificance because it has been identified in 1.9% (148/7908) of South Asian chro mosomes with 5 homozygotes by the Exome Aggregation Consortium (ExAC, http://exa; dbSNP rs146739496).
PreventionGenetics,PreventionGenetics RCV000155145 SCV000316010 benign not specified criteria provided, single submitter clinical testing
Counsyl RCV000415314 SCV000790111 likely benign Deafness, autosomal recessive 77 2017-03-06 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000155145 SCV000859147 likely benign not specified 2018-01-26 criteria provided, single submitter clinical testing
GeneDx RCV000839248 SCV000981137 benign not provided 2018-05-04 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 RCV000839248 SCV001037675 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000415314 SCV001281844 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.
Baylor Genetics RCV000415314 SCV000328766 uncertain significance Deafness, autosomal recessive 77 2016-01-29 no assertion criteria provided clinical testing Our laboratory reported dual molecular diagnoses in PUF60 (NM_001271099.1, c.1381-2A>G) and LOXHD1 (NM_144612.6, c.4217C>T and c.442A>T in trans) in one individual with reported features which include delayed motor milestones, delayed speech, intellectual disability, bilateral sensorineural hearing loss, febrile seizures, dysmorphic features, short stature, failure to thrive, and abnormal visual tracking. Heterozygotes for the LOXHD1 variants would not be expected to be affected.

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