ClinVar Miner

Submissions for variant NM_052867.4(NALCN):c.3553G>A (p.Ala1185Thr)

dbSNP: rs2139519168
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV002226143 SCV002504568 pathogenic not provided 2022-04-23 criteria provided, single submitter clinical testing Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28333917)
3billion RCV002250800 SCV002521313 pathogenic Congenital contractures of the limbs and face, hypotonia, and developmental delay 2022-05-22 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. It is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.80; 3Cnet: 0.73). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with NALCN related disorder (PMID: 28333917). The variant has been previously reported as de novo in a similarly affected individual (PMID: 28333917). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
CeGaT Center for Human Genetics Tuebingen RCV002226143 SCV003917295 likely pathogenic not provided 2023-01-01 criteria provided, single submitter clinical testing NALCN: PM1, PM2, PP2, PP3, PS2:Supporting, PS4:Supporting

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