ClinVar Miner

Submissions for variant NM_014284.3(NCDN):c.565G>A (p.Gly189Ser)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV004109067 SCV003578242 uncertain significance not specified 2021-12-03 criteria provided, single submitter clinical testing The c.565G>A (p.G189S) alteration is located in exon 3 (coding exon 3) of the NCDN gene. This alteration results from a G to A substitution at nucleotide position 565, causing the glycine (G) at amino acid position 189 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Neuberg Centre For Genomic Medicine, NCGM RCV004818261 SCV005438994 uncertain significance Neurodevelopmental disorder with infantile epileptic spasms 2023-07-22 criteria provided, single submitter clinical testing The missense c.565G>Ap.Gly189Ser variant in NCDN gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Gly189Ser variant is present with allele frequency of 0.004% in gnomAD Exomes. This variant has not been submitted to the ClinVar database. Multiple lines of computational evidences Polyphen - Possibly damaging, SIFT - Tolerated and MutationTaster - Disease causing predict conflicting evidence on protein structure and function for this variant. The reference amino acid at this position on NCDN gene is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Gly at position 189 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance VUS.
PreventionGenetics, part of Exact Sciences RCV004756477 SCV005366356 likely benign NCDN-related disorder 2024-08-28 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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