ClinVar Miner

Submissions for variant NM_014489.4(PGAP2):c.615T>A (p.Asn205Lys)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002789626 SCV003757339 uncertain significance Inborn genetic diseases 2022-02-10 criteria provided, single submitter clinical testing The c.615T>A (p.N205K) alteration is located in exon 5 (coding exon 4) of the PGAP2 gene. This alteration results from a T to A substitution at nucleotide position 615, causing the asparagine (N) at amino acid position 205 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Neuberg Centre For Genomic Medicine, NCGM RCV003340658 SCV004048395 uncertain significance Hyperphosphatasia with intellectual disability syndrome 3 criteria provided, single submitter clinical testing The missense variant c.786T>A (p.Asn262Lys) in PGAP2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Asn262Lys variant is reported with the allele frequency (0.01%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The amino acid Asn at position 262 is changed to a Lys changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by PolyPhen2 and the residue is conserved across species. The amino acid change p.Asn262Lys in PGAP2 is predicted as conserved by GERP++. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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