ClinVar Miner

Submissions for variant NM_015631.6(TCTN3):c.1196G>A (p.Ser399Asn)

gnomAD frequency: 0.00001  dbSNP: rs768285987
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000794557 SCV000933972 uncertain significance Orofacial-digital syndrome IV; Joubert syndrome 18 2021-08-24 criteria provided, single submitter clinical testing This sequence change replaces serine with asparagine at codon 399 of the TCTN3 protein (p.Ser399Asn). The serine residue is highly conserved and there is a small physicochemical difference between serine and asparagine. This variant is present in population databases (rs768285987, ExAC 0.003%). This variant has not been reported in the literature in individuals affected with TCTN3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV003243300 SCV003942906 uncertain significance Inborn genetic diseases 2023-06-01 criteria provided, single submitter clinical testing The c.1196G>A (p.S399N) alteration is located in exon 10 (coding exon 10) of the TCTN3 gene. This alteration results from a G to A substitution at nucleotide position 1196, causing the serine (S) at amino acid position 399 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Fulgent Genetics, Fulgent Genetics RCV000794557 SCV005678463 uncertain significance Orofacial-digital syndrome IV; Joubert syndrome 18 2024-05-08 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004740452 SCV005362411 uncertain significance TCTN3-related disorder 2024-09-29 no assertion criteria provided clinical testing The TCTN3 c.1196G>A variant is predicted to result in the amino acid substitution p.Ser399Asn. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0054% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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