ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.753G>T (p.Glu251Asp)

gnomAD frequency: 0.00002  dbSNP: rs751316371
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000680075 SCV000807515 uncertain significance Muscle eye brain disease 2017-09-01 criteria provided, single submitter clinical testing Possible pathogenicity based on finding it once in our laboratory with another variant (phase undetermined) in a newborn male with possible Walker-Warburg syndrome (hydrocephaly, kinked brainstem, cobblestone lissencephaly, multiple VSDs, possible anomalous pulmonary venous return), similarly affected prior pregnancy in mom (not tested)
GeneDx RCV001775949 SCV002012868 uncertain significance not provided 2019-03-15 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 25326635)
Labcorp Genetics (formerly Invitae), Labcorp RCV001868301 SCV002111295 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2022-07-27 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 251 of the POMGNT1 protein (p.Glu251Asp). This variant is present in population databases (rs751316371, gnomAD 0.03%). 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: 561091). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 RCV001775949 SCV003811729 uncertain significance not provided 2022-04-20 criteria provided, single submitter clinical testing

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