ClinVar Miner

Submissions for variant NM_000246.4(CIITA):c.3217T>A (p.Ser1073Thr)

gnomAD frequency: 0.00003  dbSNP: rs761139192
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000692230 SCV000820042 uncertain significance MHC class II deficiency 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 1073 of the CIITA protein (p.Ser1073Thr). This variant is present in population databases (rs761139192, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CIITA-related conditions. ClinVar contains an entry for this variant (Variation ID: 571174). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002060875 SCV002496053 uncertain significance MHC class II deficiency; Rheumatoid arthritis 2022-02-08 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in 0.02% (4/15288) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/16-10922234-T-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:571174). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Natera, Inc. RCV000692230 SCV002093763 uncertain significance MHC class II deficiency 2019-10-28 no assertion criteria provided clinical testing

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