ClinVar Miner

Submissions for variant NM_032237.5(POMK):c.254A>G (p.Lys85Arg)

gnomAD frequency: 0.00001  dbSNP: rs752925552
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000555005 SCV000654035 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12; Limb-girdle muscular dystrophy due to POMK deficiency 2021-09-01 criteria provided, single submitter clinical testing This sequence change replaces lysine with arginine at codon 85 of the POMK protein (p.Lys85Arg). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and arginine. This variant is present in population databases (rs752925552, ExAC 0.005%). This variant has not been reported in the literature in individuals affected with POMK-related conditions. ClinVar contains an entry for this variant (Variation ID: 474190). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C25". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
GeneDx RCV001755894 SCV001986998 uncertain significance not provided 2019-05-15 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV003243193 SCV003952097 uncertain significance Inborn genetic diseases 2023-04-19 criteria provided, single submitter clinical testing The c.254A>G (p.K85R) alteration is located in exon 4 (coding exon 1) of the POMK gene. This alteration results from a A to G substitution at nucleotide position 254, causing the lysine (K) at amino acid position 85 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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