ClinVar Miner

Submissions for variant NM_022773.4(LMF1):c.1391G>A (p.Trp464Ter)

gnomAD frequency: 0.00001  dbSNP: rs587777626
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000133508 SCV001521479 pathogenic Lipase deficiency, combined 2020-01-17 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Revvity Omics, Revvity RCV000133508 SCV002017152 pathogenic Lipase deficiency, combined 2019-06-06 criteria provided, single submitter clinical testing
Mendelics RCV000133508 SCV002517567 pathogenic Lipase deficiency, combined 2022-05-04 criteria provided, single submitter clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV000133508 SCV004808293 pathogenic Lipase deficiency, combined 2024-03-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV004992012 SCV005614239 pathogenic Cardiovascular phenotype 2024-11-05 criteria provided, single submitter clinical testing The c.1391G>A (p.W464*) alteration, located in exon 9 (coding exon 9) of the LMF1 gene, consists of a G to A substitution at nucleotide position 1391. This changes the amino acid from a tryptophan (W) to a stop codon at amino acid position 464. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the A allele has an overall frequency of <0.001% (1/246870) total alleles studied. The highest observed frequency was 0.005% (1/21230) of Finnish alleles. This variant has been identified in the homozygous state in one individual with severe hypertriglyceridemia noted with an episode of acute pancreatitis (Cefal&ugrave;, 2009). Based on the available evidence, this alteration is classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV005089661 SCV005837245 pathogenic not provided 2024-08-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Trp464*) 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 present in population databases (no rsID available, gnomAD 0.005%). This premature translational stop signal has been observed in individual(s) with clinical features of chylomicronemia (PMID: 19820022, 30037590). ClinVar contains an entry for this variant (Variation ID: 143993). Algorithms developed to predict the effect of variants on gene product 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: 30037590). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000133508 SCV000188582 pathogenic Lipase deficiency, combined 2009-11-01 no assertion criteria provided literature only
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000133508 SCV001469203 pathogenic Lipase deficiency, combined 2020-09-10 no assertion criteria provided clinical testing

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