ClinVar Miner

Submissions for variant NM_000246.4(CIITA):c.286G>A (p.Ala96Thr)

gnomAD frequency: 0.00046  dbSNP: rs149253747
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000634010 SCV000755284 uncertain significance MHC class II deficiency 2022-08-19 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 96 of the CIITA protein (p.Ala96Thr). This variant is present in population databases (rs149253747, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. 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: 528783). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; 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 RCV005407828 SCV002496054 uncertain significance Rheumatoid arthritis; MHC class II deficiency 1 criteria provided, single submitter clinical testing CIITA NM_000246.3 exon 3 p.Ala96Thr (c.286G>A):This variant has not been reported in the literature but is present in 0.08% (60/68036) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/16-10895755-G-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:528783). Evolutionary conservation for this variant is unclear; 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.
Ambry Genetics RCV002533188 SCV003568145 uncertain significance Inborn genetic diseases 2024-01-02 criteria provided, single submitter clinical testing The c.286G>A (p.A96T) alteration is located in exon 3 (coding exon 3) of the CIITA gene. This alteration results from a G to A substitution at nucleotide position 286, causing the alanine (A) at amino acid position 96 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Breakthrough Genomics, Breakthrough Genomics RCV004691970 SCV005194217 uncertain significance not provided criteria provided, single submitter not provided
Natera, Inc. RCV000634010 SCV001462162 uncertain significance MHC class II deficiency 2019-12-10 no assertion criteria provided clinical testing

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