ClinVar Miner

Submissions for variant NM_032776.3(JMJD1C):c.4913C>T (p.Ser1638Leu)

gnomAD frequency: 0.00024  dbSNP: rs143177790
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000818756 SCV000959386 uncertain significance Early myoclonic encephalopathy 2023-11-24 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 1638 of the JMJD1C protein (p.Ser1638Leu). This variant is present in population databases (rs143177790, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with JMJD1C-related conditions. ClinVar contains an entry for this variant (Variation ID: 661359). 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 JMJD1C 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.
New York Genome Center RCV001784444 SCV002025612 uncertain significance not provided 2020-06-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV004629349 SCV005127353 uncertain significance not specified 2024-03-31 criteria provided, single submitter clinical testing The c.4913C>T (p.S1638L) alteration is located in exon 10 (coding exon 10) of the JMJD1C gene. This alteration results from a C to T substitution at nucleotide position 4913, causing the serine (S) at amino acid position 1638 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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