ClinVar Miner

Submissions for variant NM_006118.4(HAX1):c.757C>A (p.Pro253Thr)

gnomAD frequency: 0.00004  dbSNP: rs149721308
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001241157 SCV001414153 uncertain significance Kostmann syndrome 2022-10-26 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 253 of the HAX1 protein (p.Pro253Thr). This variant is present in population databases (rs149721308, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with HAX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 966471). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Ambry Genetics RCV003353254 SCV004064979 uncertain significance Inborn genetic diseases 2024-10-02 criteria provided, single submitter clinical testing The p.P253T variant (also known as c.757C>A), located in coding exon 7 of the HAX1 gene, results from a C to A substitution at nucleotide position 757. The proline at codon 253 is replaced by threonine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV003883587 SCV004701756 uncertain significance not provided 2023-12-01 criteria provided, single submitter clinical testing HAX1: PM2, BP4
Natera, Inc. RCV001241157 SCV002086440 uncertain significance Kostmann syndrome 2020-02-13 no assertion criteria provided clinical testing

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