ClinVar Miner

Submissions for variant NM_003801.4(GPAA1):c.1658C>T (p.Pro553Leu)

gnomAD frequency: 0.00005  dbSNP: rs372282426
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001336604 SCV001530031 uncertain significance Glycosylphosphatidylinositol biosynthesis defect 15 2018-07-31 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV001865852 SCV002196285 uncertain significance not provided 2024-10-12 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 553 of the GPAA1 protein (p.Pro553Leu). This variant is present in population databases (rs372282426, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with GPAA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1034026). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt GPAA1 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV004629582 SCV005126505 uncertain significance Inborn genetic diseases 2024-04-15 criteria provided, single submitter clinical testing The c.1658C>T (p.P553L) alteration is located in exon 12 (coding exon 12) of the GPAA1 gene. This alteration results from a C to T substitution at nucleotide position 1658, causing the proline (P) at amino acid position 553 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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