ClinVar Miner

Submissions for variant NM_000416.3(IFNGR1):c.653_655del (p.Glu218del)

dbSNP: rs587776858
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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 RCV002228043 SCV000951645 uncertain significance Disseminated atypical mycobacterial infection 2022-03-19 criteria provided, single submitter clinical testing This variant is also known as 652del3. This variant, c.653_655del, results in the deletion of 1 amino acid(s) of the IFNGR1 protein (p.Glu218del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs587776858, gnomAD 0.003%). This variant has been observed in individual(s) with autosomal recessive Mendelian susceptibility to mycobacterial disease (MSMD) due to interferon-gamma receptor 1 deficiency (PMID: 10811850, 26173802). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 17951). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects IFNGR1 function (PMID: 10811850, 26173802). 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.
3billion, Medical Genetics RCV000019547 SCV002318540 uncertain significance Immunodeficiency 27A 2022-03-22 criteria provided, single submitter clinical testing Inframe deletion located in a nonrepeat region: predicted to change the length of the protein and disrupt normal protein function(PM4_M). This variant has been reported as pathogenic (PMID:10811850). The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0000040). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.
OMIM RCV000019547 SCV000039844 pathogenic Immunodeficiency 27A 2000-05-01 no assertion criteria provided literature only

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