ClinVar Miner

Submissions for variant NM_006268.5(DPF2):c.900C>T (p.Arg300=)

gnomAD frequency: 0.00001  dbSNP: rs775695232
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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 RCV001591703 SCV001815741 uncertain significance Coffin-Siris syndrome 7 2020-11-17 criteria provided, single submitter clinical testing The c.900C>T (p.Arg300=) variant identified in the DPF2 gene is a synonymous variant at amino acid 300/392. The Cytosine at this position is well conserved throughout mammals. While Splice AI does not predict an alteration to splicing, the Transcript inferred Pathogenicity Score (TraP) for this position is 0.381, which is >95% score-percentile for coding variants suggesting it is possibly damaging. The c.900C>T (p.Arg300=) variant is found with low frequency in gnomAD(v3.1) (2 heterozygotes, 0 homozygotes; allele frequency: 1.3e-5), suggesting it is not a common benign variant in the populations represented in that database. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. Given the lack of compelling evidence for its pathogenicity, the c.900C>T (p.Arg300=) variant identified in the DPF2 gene is reported as a Variant of Uncertain Significance.

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