ClinVar Miner

Submissions for variant NM_015202.5(KATNIP):c.2849C>T (p.Ser950Leu)

gnomAD frequency: 0.00063  dbSNP: rs71389806
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV001839328 SCV002099325 uncertain significance Joubert syndrome 26 2021-07-07 criteria provided, single submitter clinical testing The c.2849C>T (p.Ser950Leu) inherited variant in exon 16 of 28 of KATNIP has not been reported in affected individuals in the available literature. This variant is absent in gnomAD v3 indicating it is not a common benign variant in the populations represented in this database. In silico predictors suggest this variant isBenign (REVEL score: 0.008) and Tolerated (SIFT score: 0.32). Given the current evidence regarding its pathogenicity, the c.2849C>T (p.Ser950Leu) variant identified in the KATNIP gene is classified as a Variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV002545224 SCV003279123 uncertain significance not provided 2024-10-28 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 950 of the KIAA0556 protein (p.Ser950Leu). This variant is present in population databases (rs71389806, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with KIAA0556-related conditions. ClinVar contains an entry for this variant (Variation ID: 1342577). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV004041047 SCV004890554 likely benign not specified 2021-12-16 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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