ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.589_590del (p.Pro197fs)

dbSNP: rs763591247
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001009084 SCV001168894 likely pathogenic not provided 2018-10-09 criteria provided, single submitter clinical testing A variant that is likely pathogenic has been identified in the PIGO gene. The c.589_590delCC variant is not observed in large population cohorts (Lek et al., 2016). The c.589_590delCC variant causes a frameshift starting with codon Proline 197, changes this amino acid to an Isoleucine residue and creates a premature Stop codon at position 26 of the new reading frame, denoted p.Pro197IlefsX26. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. This variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Labcorp Genetics (formerly Invitae), Labcorp RCV000779580 SCV002246691 pathogenic Hyperphosphatasia with intellectual disability syndrome 2 2024-08-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Pro197Ilefs*26) in the PIGO gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PIGO are known to be pathogenic (PMID: 22683086, 24417746). This variant is present in population databases (rs763591247, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. ClinVar contains an entry for this variant (Variation ID: 632540). For these reasons, this variant has been classified as Pathogenic.

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