ClinVar Miner

Submissions for variant NM_032237.5(POMK):c.910T>C (p.Phe304Leu)

gnomAD frequency: 0.00008  dbSNP: rs757744253
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000533624 SCV000654053 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12; Limb-girdle muscular dystrophy due to POMK deficiency 2024-01-15 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 304 of the POMK protein (p.Phe304Leu). This variant is present in population databases (rs757744253, gnomAD 0.1%). 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: 474199). 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 POMK protein function with a negative predictive value of 80%. 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 RCV001539577 SCV001757365 uncertain significance not provided 2020-12-02 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001539577 SCV003811793 uncertain significance not provided 2023-11-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV003159920 SCV003877808 uncertain significance Inborn genetic diseases 2023-01-26 criteria provided, single submitter clinical testing The c.910T>C (p.F304L) alteration is located in exon 5 (coding exon 2) of the POMK gene. This alteration results from a T to C substitution at nucleotide position 910, causing the phenylalanine (F) at amino acid position 304 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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