ClinVar Miner

Submissions for variant NM_006118.4(HAX1):c.91del (p.Glu31fs)

gnomAD frequency: 0.00026  dbSNP: rs764082747
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485748 SCV000568065 pathogenic not provided 2024-05-04 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 19036076, 34426522, 31589614, 32054657, 19499579)
Labcorp Genetics (formerly Invitae), Labcorp RCV000706106 SCV000835138 pathogenic Kostmann syndrome 2024-01-30 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. Loss-of-function variants in HAX1 are known to be pathogenic (PMID: 17187068). This variant is present in population databases (rs764082747, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with severe congenital neutropenia (PMID: 19036076, 19499579). ClinVar contains an entry for this variant (Variation ID: 419887). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Clinical Genetics and Genomics, Karolinska University Hospital RCV000485748 SCV001450266 likely pathogenic not provided 2014-12-18 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000706106 SCV002024945 pathogenic Kostmann syndrome 2023-10-19 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000485748 SCV002098330 pathogenic not provided 2022-01-25 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000485748 SCV002502270 pathogenic not provided 2022-03-18 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000706106 SCV002782074 pathogenic Kostmann syndrome 2024-05-03 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003155204 SCV003845036 pathogenic Severe congenital neutropenia 2023-02-20 criteria provided, single submitter clinical testing Variant summary: HAX1 c.91delG (p.Glu31LysfsX54) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 0.00019 in 251294 control chromosomes. This frequency is not higher than estimated for a pathogenic variant in HAX1 causing Severe Congenital Neutropenia (0.00019 vs 0.00079), allowing no conclusion about variant significance. c.91delG has been reported in the literature in individuals affected with Severe Congenital Neutropenia (e.g. Smith_2009, Carlsson_2012). These data indicate that the variant is likely to be associated with disease. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV000706106 SCV005085941 pathogenic Kostmann syndrome 2024-09-20 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with severe congenital neutropenia 3 (MIM#610738). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 58 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in individuals with neutropenia and classified as pathogenic in ClinVar (PMID: 37193639). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Clinical Genetics Laboratory, Skane University Hospital Lund RCV000485748 SCV005198426 pathogenic not provided 2022-05-27 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000485748 SCV005413729 pathogenic not provided 2024-05-30 criteria provided, single submitter clinical testing PM3_strong, PVS1
OMIM RCV000706106 SCV000025096 pathogenic Kostmann syndrome 2009-03-01 no assertion criteria provided literature only
Natera, Inc. RCV000706106 SCV001461732 pathogenic Kostmann syndrome 2020-09-16 no assertion criteria provided clinical testing

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