ClinVar Miner

Submissions for variant NM_015047.3(EMC1):c.797T>G (p.Leu266Ter)

gnomAD frequency: 0.00001  dbSNP: rs1277233450
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001921459 SCV002199248 pathogenic not provided 2025-01-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu266*) in the EMC1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EMC1 are known to be pathogenic (PMID: 26572623, 26942288, 29271071). This variant is present in population databases (no rsID available, gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EMC1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1424185). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001921459 SCV005334430 likely pathogenic not provided 2024-03-26 criteria provided, single submitter clinical testing Reported along with a second variant on the opposite allele (in trans) in a patient with psychomotor developmental delay (PMID: 35183220); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 35183220)
Ambry Genetics RCV004975898 SCV005575228 pathogenic Inborn genetic diseases 2024-07-10 criteria provided, single submitter clinical testing The c.797T>G (p.L266*) alteration, located in exon 8 (coding exon 8) of the EMC1 gene, consists of a T to G substitution at nucleotide position 797. This changes the amino acid from a leucine (L) to a stop codon at amino acid position 266. 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 G allele has an overall frequency of 0.001% (3/281346) total alleles studied. This variant has been identified in trans with another EMC1 variant in an individual with psychomotor development delay (Álvarez-Mora, 2022). Based on the available evidence, this alteration is classified as pathogenic.

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