ClinVar Miner

Submissions for variant NM_015570.4(AUTS2):c.1673C>T (p.Thr558Met)

gnomAD frequency: 0.00001  dbSNP: rs552275264
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV002266785 SCV002548886 uncertain significance Autism spectrum disorder due to AUTS2 deficiency 2021-08-12 criteria provided, single submitter clinical testing The c.1673C>T (p.Thr558Met) variant identified in the AUTS2 gene substitutes a well conserved Threonine for Methionine at amino acid 558/1260(exon 9/19). This variant is found with low frequency in gnomAD(v2.1.1)(3 heterozygotes, 0 homozygotes; allele frequency: 1.21e-5) suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be Damaging (SIFT; score:0.026) and Benign (REVEL;score:0.2189) to the function of the canonical transcript. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. The p.Thr558 residue is not within a mapped domain of AUTS2 (UniProtKB:Q8WXX7). Given the lack of compelling evidence for its pathogenicity, the c.1673C>T (p.Thr558Met) variant identified in the AUTS2 gene is reported as a Variant of Uncertain Significance.

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