ClinVar Miner

Submissions for variant NM_000182.5(HADHA):c.1072C>A (p.Gln358Lys)

gnomAD frequency: 0.02193  dbSNP: rs2229420
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224809 SCV000281661 benign not provided 2016-04-25 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000320111 SCV000429519 likely benign Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services, Illumina RCV000377268 SCV000429520 likely benign Mitochondrial trifunctional protein deficiency 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Invitae RCV001081747 SCV000645771 benign Mitochondrial trifunctional protein deficiency; Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency 2024-01-31 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000594589 SCV000704871 benign not specified 2017-01-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000594589 SCV000917469 benign not specified 2018-07-12 criteria provided, single submitter clinical testing Variant summary: HADHA c.1072C>A (p.Gln358Lys) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0076 in 277056 control chromosomes in the gnomAD database, including 67 homozygotes. The observed variant frequency is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in HADHA causing Long Chain 3-Hydroxyacyl-CoA Dehydrogenase Deficiency phenotype (0.0019), strongly suggesting that the variant is benign. The variant c.1072C>A has been reported in the literature in an individual affected with mitochondrial trifunctional protein deficiency, however other variants were also present in this patient that could explain the observed phenotype (Djouadi 2016). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV000224809 SCV001845416 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 15533621, 21228398, 20981092)
Natera, Inc. RCV000320111 SCV001462516 benign Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency 2020-09-16 no assertion criteria provided clinical testing

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