ClinVar Miner

Submissions for variant NM_021008.4(DEAF1):c.926del (p.Leu309fs)

dbSNP: rs1417226023
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002222872 SCV002500104 likely pathogenic Intellectual disability, autosomal dominant 24 2022-03-04 criteria provided, single submitter clinical testing Variant summary: DEAF1 c.926delT (p.Leu309ArgfsX6) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4e-06 in 251490 control chromosomes (gnomAD). To our knowledge, no occurrence of c.926delT in individuals affected with Mental Retardation, Autosomal Dominant 24 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV003089145 SCV003021741 pathogenic not provided 2023-09-30 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu309Argfs*6) in the DEAF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DEAF1 are known to be pathogenic (PMID: 30923367). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with DEAF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1677014). For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences RCV004529102 SCV004112774 likely pathogenic DEAF1-related disorder 2023-03-23 criteria provided, single submitter clinical testing The DEAF1 c.926delT variant is predicted to result in a frameshift and premature protein termination (p.Leu309Argfs*6). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD ( Frameshift variants in DEAF1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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