ClinVar Miner

Submissions for variant NM_000246.4(CIITA):c.1765G>A (p.Glu589Lys)

dbSNP: rs2039233689
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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 RCV001320379 SCV001511161 uncertain significance MHC class II deficiency 2022-04-12 criteria provided, single submitter clinical testing 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. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 589 of the CIITA protein (p.Glu589Lys). This variant is not present in population databases (gnomAD no frequency). 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: 1020749). 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.
Ambry Genetics RCV004978319 SCV005559416 uncertain significance Inborn genetic diseases 2024-10-16 criteria provided, single submitter clinical testing The c.1765G>A (p.E589K) alteration is located in exon 11 (coding exon 11) of the CIITA gene. This alteration results from a G to A substitution at nucleotide position 1765, causing the glutamic acid (E) at amino acid position 589 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001320379 SCV002093708 uncertain significance MHC class II deficiency 2021-02-10 no assertion criteria provided clinical testing

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