ClinVar Miner

Submissions for variant NM_000235.4(LIPA):c.46A>C (p.Thr16Pro)

gnomAD frequency: 0.25399  dbSNP: rs1051338
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175562 SCV000227070 benign not specified 2015-03-27 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000175562 SCV000303105 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000350905 SCV000366006 benign Wolman disease 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000606750 SCV000366007 benign Lysosomal acid lipase deficiency 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000350905 SCV001729013 benign Wolman disease 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000606750 SCV001754873 benign Lysosomal acid lipase deficiency 2021-07-10 criteria provided, single submitter clinical testing
GeneDx RCV000675918 SCV001893547 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 22395809, 31645127, 29196158, 28279971)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000175562 SCV002051172 likely benign not specified 2021-12-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV002336425 SCV002640015 benign Cardiovascular phenotype 2018-12-11 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GENinCode PLC RCV000606750 SCV005068276 benign Lysosomal acid lipase deficiency 2022-07-06 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000675918 SCV005221893 likely benign not provided criteria provided, single submitter not provided
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000606750 SCV000732966 benign Lysosomal acid lipase deficiency no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675918 SCV000801645 benign not provided 2015-10-23 no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000175562 SCV001920725 benign not specified no assertion criteria provided clinical testing
Natera, Inc. RCV000606750 SCV002091532 benign Lysosomal acid lipase deficiency 2019-11-20 no assertion criteria provided clinical testing

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