ClinVar Miner

Submissions for variant NM_024989.4(PGAP1):c.2042del (p.Leu681fs)

gnomAD frequency: 0.00004  dbSNP: rs756609752
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Leipzig Medical Center RCV001262862 SCV001440890 likely pathogenic Intellectual disability, autosomal recessive 42 2019-01-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001262862 SCV002231956 pathogenic Intellectual disability, autosomal recessive 42 2024-10-17 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu681Argfs*4) in the PGAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PGAP1 are known to be pathogenic (PMID: 17711852, 26050939, 27848944). This variant is present in population databases (rs756609752, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PGAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 983046). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV002537640 SCV003698269 pathogenic Inborn genetic diseases 2022-05-09 criteria provided, single submitter clinical testing The c.2042delT (p.L681Rfs*4) alteration, located in exon 22 (coding exon 22) of the PGAP1 gene, consists of a deletion of one nucleotide at position 2042, causing a translational frameshift with a predicted alternate stop codon after 4 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on the available evidence, this alteration is classified as pathogenic.

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