ClinVar Miner

Submissions for variant NM_001018837.2(HAX1):c.54-107del (rs764082747)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485748 SCV000568065 pathogenic not provided 2017-02-20 criteria provided, single submitter clinical testing The c.91delG pathogenic variant in the HAX1 gene has been reported previously in association with severe congenital neutropenia (SCN) (Carlsson et al., 2009; Smith et al., 2009). The deletion causes a frameshift starting with codon Glutamic acid 31, changes this amino acid to a Lysine residue and creates a premature Stop codon at position 54 of the new reading frame, denoted p.Glu31LysfsX54. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In addition, the variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In summary, we consider this variant to be pathogenic.
Invitae RCV000706106 SCV000835138 pathogenic Severe congenital neutropenia 3, autosomal recessive 2018-08-15 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu31Lysfs*54) in the HAX1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs764082747, ExAC 0.02%). This variant has been reported in individuals affected with severe congenital neutropenia (PMID: 19036076, 19499579). ClinVar contains an entry for this variant (Variation ID: 419887). Loss-of-function variants in HAX1 are known to be pathogenic (PMID: 17187068). For these reasons, this variant has been classified as Pathogenic.

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