ClinVar Miner

Submissions for variant NM_024989.4(PGAP1):c.1396C>T (p.Gln466Ter)

gnomAD frequency: 0.00001  dbSNP: rs143038880
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV003128596 SCV003805381 likely pathogenic not provided 2023-02-15 criteria provided, single submitter clinical testing Observed with a second loss-of-function PGAP1 variant on the opposite allele (in trans) in a male child with cortical visual impairment, hypotonia, and global developmental delay (Williams et al., 2015); 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 a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27206732, 26563290, 25823418, 33198937)
Duke University Health System Sequencing Clinic, Duke University Health System RCV000208575 SCV003919047 pathogenic Intellectual disability, autosomal recessive 42 2023-04-20 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV000208575 SCV004500003 pathogenic Intellectual disability, autosomal recessive 42 2023-05-26 criteria provided, single submitter clinical testing This variant is present in population databases (rs143038880, gnomAD 0.003%). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 222978). This premature translational stop signal has been observed in individual(s) with clinical features of autosomal recessive PGAP1-related condition (PMID: 25823418). This sequence change creates a premature translational stop signal (p.Gln466*) 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).
OMIM RCV000208575 SCV000264355 pathogenic Intellectual disability, autosomal recessive 42 2021-05-24 no assertion criteria provided literature only

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