ClinVar Miner

Submissions for variant NM_016648.4(LARP7):c.1213dup (p.Thr405fs)

dbSNP: rs750946801
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000442915 SCV000510984 likely pathogenic not provided 2016-07-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000442915 SCV002962703 pathogenic not provided 2022-06-10 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 376972). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with LARP7-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Thr405Asnfs*26) in the LARP7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LARP7 are known to be pathogenic (PMID: 22865833, 26374271, 26607181).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005238977 SCV005886268 pathogenic Microcephalic primordial dwarfism, Alazami type 2025-02-06 criteria provided, single submitter clinical testing Variant summary: LARP7 c.1213dupA (p.Thr405AsnfsX26) 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 frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. To our knowledge, no occurrence of c.1213dupA in individuals affected with Microcephalic Primordial Dwarfism, Alazami Type and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 376972). Based on the evidence outlined above, the variant was classified as pathogenic.

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