ClinVar Miner

Submissions for variant NM_000433.3(NCF2):c.55_63del (p.Lys19_Asp21del) (rs796065033)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000494542 SCV000582904 pathogenic not provided 2017-05-15 criteria provided, single submitter clinical testing The c.55_63delAAGAAGGAC variant has been published previously in association with CGD (Noack et al., 1999; Patiño et al., 1999; Yu et al., 2008). The variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The variant results in the in-frame deletion of codons 19-21, and in silico analysis predicts this variant is probably damaging to the protein structure/function. In summary, we consider this variant to be pathogenic.
Invitae RCV000002333 SCV000956351 likely pathogenic Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2 2018-10-20 criteria provided, single submitter clinical testing This variant, c.55_63delAAGAAGGAC, results in the deletion of 3 amino acid(s) of the NCF2 protein (p.Lys19_Asp21del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed on the opposite chromosome (in trans) from other pathogenic variants in individuals affected with chronic granulomatous disease (PMID: 10498624, 10598813, 18625437). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 2245). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
OMIM RCV000002333 SCV000022491 pathogenic Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2 1999-10-01 no assertion criteria provided literature only

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