ClinVar Miner

Submissions for variant NR_023343.3(RNU4ATAC):n.116A>G

dbSNP: rs982261295
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Undiagnosed Diseases Network, NIH RCV001090145 SCV001245591 likely pathogenic Roifman syndrome 2019-10-02 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002555934 SCV003524680 likely pathogenic not provided 2023-01-18 criteria provided, single submitter clinical testing This variant occurs in the RNU4ATAC gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has been observed in individual(s) with Roifman syndrome (PMID: 29263834; external communication). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 870579). This variant is located within the Sm protein-binding region of the RNU4ATAC RNA, which is important for small nuclear RNA maturation (PMID: 32628740). A significant number of disease-associated RNU4ATAC variants are found in this region (PMID: 32628740, 30368667). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003396739 SCV004119337 likely pathogenic RNU4ATAC-related disorder 2022-12-08 criteria provided, single submitter clinical testing The RNU4ATAC n.116A>G is a noncoding alteration. This variant in the compound heterozygous condition was reported in at least two individuals with Roifman syndrome (Figure 5, Schejter et al 2017. PubMed ID: 29263834; Table 1, Benoit-Pilven et al 2020. PubMed ID: 32628740; Hallermayr et al. 2018. PubMed ID: 30455926). This variant is reported in 0.0061% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-122288571-A-G). Different variants affecting the same nucleotide (n.116A>T and n.116A>C) were also reported to be pathogenic (Table 1, Benoit-Pilven et al 2020. PubMed ID: 32628740). This variant is interpreted as likely pathogenic.

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