ClinVar Miner

Submissions for variant NM_022773.4(LMF1):c.295C>T (p.Gln99Ter)

gnomAD frequency: 0.00009  dbSNP: rs752473648
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
AiLife Diagnostics, AiLife Diagnostics RCV002224242 SCV002502354 likely pathogenic not provided 2022-01-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002434605 SCV002751519 uncertain significance Cardiovascular phenotype 2021-08-03 criteria provided, single submitter clinical testing The p.Q99* variant (also known as c.295C>T), located in coding exon 2 of the LMF1 gene, results from a C to T substitution at nucleotide position 295. This changes the amino acid from a glutamine to a stop codon within coding exon 2. This alteration would be expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. However, this region of the LMF1 gene is excluded from other transcripts which could be biologically relevant, and it is not clear if these alternative transcripts rescue the function of the protein. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003418408 SCV004117956 likely pathogenic LMF1-related disorder 2022-10-10 criteria provided, single submitter clinical testing The LMF1 c.295C>T variant is predicted to result in premature protein termination (p.Gln99*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-1004565-G-A). Nonsense variants in LMF1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV002224242 SCV004277622 pathogenic not provided 2023-09-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln99*) 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 (rs752473648, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with LMF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1677500). For these reasons, this variant has been classified as Pathogenic.

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