ClinVar Miner

Submissions for variant NM_003901.4(SGPL1):c.1483C>T (p.Arg495Ter)

gnomAD frequency: 0.00001  dbSNP: rs374024951
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology RCV001527391 SCV001738383 pathogenic Nephrotic syndrome 14 2021-02-08 criteria provided, single submitter clinical testing The c.1483C>T variant is not present in publicly available population databases like 1000 Genomes. The heterozygous state of the variant is present inExome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD) and dbSNP at a very low frequency. The variant is not present in Indian Exome Database [Kausthubham et al. Hum Mutat, 2021] or in our in-house exome database. The variant has not been previously reported to ClinVar, Human Genome Mutation Database (HGMD) or OMIM databases. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome etc. predicted this variant to be likely deleterious.
Labcorp Genetics (formerly Invitae), Labcorp RCV003771631 SCV004651714 pathogenic not provided 2024-04-25 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg495*) in the SGPL1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SGPL1 are known to be pathogenic (PMID: 28165339, 28165343). This variant is present in population databases (rs374024951, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SGPL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1173092). For these reasons, this variant has been classified as Pathogenic.
Suma Genomics RCV001527391 SCV005684997 pathogenic Nephrotic syndrome 14 criteria provided, single submitter clinical testing Stop-gain variant c.1483C>T, p.(Arg495Ter) is observed in exon 14 of SGPL1 in homozygous state. This variant is observed in 11 individuals in the gnomAD database in heterozygous state. ACMG classification: Pathogenic Criteria met: PVS1, PM2_Supporting and PP5

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