ClinVar Miner

Submissions for variant NM_017837.4(PIGV):c.115G>A (p.Glu39Lys)

gnomAD frequency: 0.00005  dbSNP: rs369275802
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001662530 SCV000617986 likely benign not provided 2018-06-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000765106 SCV000896328 uncertain significance Hyperphosphatasia with intellectual disability syndrome 1 2018-10-31 criteria provided, single submitter clinical testing
Baylor Genetics RCV000765106 SCV001522589 uncertain significance Hyperphosphatasia with intellectual disability syndrome 1 2020-01-27 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Athena Diagnostics RCV001662530 SCV001880188 uncertain significance not provided 2021-03-19 criteria provided, single submitter clinical testing
Invitae RCV001662530 SCV002142336 uncertain significance not provided 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 39 of the PIGV protein (p.Glu39Lys). This variant is present in population databases (rs369275802, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with PIGV-related conditions. ClinVar contains an entry for this variant (Variation ID: 449659). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). 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 RCV002527587 SCV003631567 uncertain significance Inborn genetic diseases 2022-07-19 criteria provided, single submitter clinical testing The c.115G>A (p.E39K) alteration is located in exon 3 (coding exon 2) of the PIGV gene. This alteration results from a G to A substitution at nucleotide position 115, causing the glutamic acid (E) at amino acid position 39 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000765106 SCV004810004 uncertain significance Hyperphosphatasia with intellectual disability syndrome 1 2024-04-04 criteria provided, single submitter clinical testing

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