ClinVar Miner

Submissions for variant NM_022773.4(LMF1):c.1317C>G (p.Tyr439Ter)

dbSNP: rs121909397
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002512620 SCV003441701 pathogenic not provided 2022-08-21 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr439*) in the LMF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LMF1 are known to be pathogenic (PMID: 17994020, 19820022, 22239554). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with combined lipase deficiency (PMID: 17994020). ClinVar contains an entry for this variant (Variation ID: 792). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects LMF1 function (PMID: 17994020). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000000828 SCV000020978 pathogenic Lipase deficiency, combined 2007-12-01 no assertion criteria provided literature only
GBinsight Genetic Testing by GB HealthWatch, Genben Lifesciences Corporation RCV000000828 SCV001314173 pathogenic Lipase deficiency, combined 2020-05-27 no assertion criteria provided clinical testing Proband referred for clinical genetic testing presented with syndrome consistent with familial chylomicronemia syndrome with severe hypertriglyceridemia, low HDL-cholesterol and type 2 diabetes. Clinical genetic testing identified homozygosity for the Cys77Tyr (NM_178172.6:c.230G>A) genetic variant in the the germline. Phenotype segregated with genotype in family members. This variant introduces a premature stop codon, which can cause nonsense-mediated decay of the mutant protein. Péterfy et al (PMID: 17994020) identified this genetic variant in patients with severe hypertriglyceridemia and classified this variant as pathogenic for LMF1 deficiency.

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