ClinVar Miner

Submissions for variant NM_005055.5(RAPSN):c.457G>A (p.Ala153Thr)

dbSNP: rs142635726
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000850591 SCV000992814 uncertain significance Fetal akinesia deformation sequence 1; Congenital myasthenic syndrome 11 2012-08-10 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001105500 SCV001262468 uncertain significance Fetal akinesia deformation sequence 1 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina RCV001105501 SCV001262469 uncertain significance Congenital myasthenic syndrome 11 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003330969 SCV004038115 uncertain significance not specified 2023-08-02 criteria provided, single submitter clinical testing Variant summary: RAPSN c.457G>A (p.Ala153Thr) results in a non-conservative amino acid change located in the MalT-like TPR region (IPR041617) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 248824 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.457G>A has been reported in the literature in heterozygous individuals affected with autism spectrum disorder and had whole exome sequencing analysis (Fu_2022 and Liu_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Congenital Myasthenic Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31216405, 35982160, 35982159). One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Baylor Genetics RCV003467530 SCV004206095 likely pathogenic Fetal akinesia deformation sequence 2 2024-02-05 criteria provided, single submitter clinical testing

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