ClinVar Miner

Submissions for variant NM_022098.4(XPNPEP3):c.388C>G (p.Pro130Ala)

gnomAD frequency: 0.00009  dbSNP: rs199693203
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001146791 SCV001307549 uncertain significance Nephronophthisis-like nephropathy 1 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001146791 SCV001607812 likely benign Nephronophthisis-like nephropathy 1 2018-11-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV004030055 SCV004979728 uncertain significance Inborn genetic diseases 2023-09-22 criteria provided, single submitter clinical testing The c.388C>G (p.P130A) alteration is located in exon 3 (coding exon 3) of the XPNPEP3 gene. This alteration results from a C to G substitution at nucleotide position 388, causing the proline (P) at amino acid position 130 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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