ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.268C>T (p.Arg90Cys)

gnomAD frequency: 0.00004  dbSNP: rs144959783
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000331025 SCV000335345 uncertain significance not provided 2016-10-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001233854 SCV001406468 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-10-31 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 90 of the POMGNT1 protein (p.Arg90Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 283329). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POMGNT1 protein function. 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.
Revvity Omics, Revvity RCV000331025 SCV003811778 uncertain significance not provided 2019-06-17 criteria provided, single submitter clinical testing
Ambry Genetics RCV004021130 SCV005007231 uncertain significance Inborn genetic diseases 2024-01-04 criteria provided, single submitter clinical testing The c.268C>T (p.R90C) alteration is located in exon 4 (coding exon 3) of the POMGNT1 gene. This alteration results from a C to T substitution at nucleotide position 268, causing the arginine (R) at amino acid position 90 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Mayo Clinic Laboratories, Mayo Clinic RCV000331025 SCV005412129 uncertain significance not provided 2024-03-28 criteria provided, single submitter clinical testing BP4
Natera, Inc. RCV001277597 SCV001464559 uncertain significance Muscle eye brain disease 2020-08-14 no assertion criteria provided clinical testing

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