Submissions for variant NM_000169.3(GLA):c.124A>C (p.Met42Leu)

gnomAD frequency: 0.00001  dbSNP: rs797044613

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000235742	SCV000293385	likely pathogenic	not provided	2024-11-13	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10666480, 17391432, 25382311, 35653365, 30386727, 15712228, 27657681, 31036492, 15492942)
Eurofins Ntd Llc (ga)	RCV000235742	SCV000331633	pathogenic	not provided	2017-06-26	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000809963	SCV000950149	pathogenic	Fabry disease	2025-01-29	criteria provided, single submitter	clinical testing	This sequence change replaces methionine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 42 of the GLA protein (p.Met42Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Fabry disease (PMID: 15492942, 15712228; http//dx.doi.org/10.16966/2380-5498.124). ClinVar contains an entry for this variant (Variation ID: 193056). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt GLA protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects GLA function (PMID: 27657681). This variant disrupts the p.Met42 amino acid residue in GLA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8875188, 12175777, 18205205, 23935525, 26415523, 27560961). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab	RCV000809963	SCV002054825	pathogenic	Fabry disease	2021-07-15	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000809963	SCV005426162	likely pathogenic	Fabry disease	2024-09-12	criteria provided, single submitter	clinical testing	This missense variant replaces methionine with leucine at codon 42 of the GLA protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). In vitro functional studies in transfected HEK-293 cells have shown that this variant causes a significant reduction in GLA activity (PMID: 27657681, 31036492). This variant has been reported in individuals affected with Fabry disease, including two with a renal variant of Fabry disease (PMID: 15492942, 15712228, 32802993; DOI:10.16966/2380-5498.124). Different variants affecting the same codon, p.Met42Val and p.Met42Thr, are considered to be disease-causing (ClinVar variation ID: 222174, 92541), suggesting that methionine at this position is important for GLA protein function. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.
Clinical Genomics Laboratory, Stanford Medicine	RCV000809963	SCV001427212	pathogenic	Fabry disease	2019-12-18	no assertion criteria provided	clinical testing	The p.Met42Leu variant in the GLA gene has been previously reported in two unrelated males with Fabry disease (Rosenthal et al., 2004; Shabbeer, Robinson & Desnick, 2005). Alpha-galactosidase A enzyme activity was tested and reported low in one of the published individuals. This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Wellestablished in vitro functional studies of p.Met42Leu variant strongly suggest a deleterious effect to the protein that is sufficient to be disease-causing (Benjamin et al., 2017; Oommen et al., 2019). Additionally, multiple different amino acid changes, p.Met42Ile, p.Met42Thr, and p.Met42Val, have been previously reported as disease-causing at this residue, which suggests another change at this residue, such as p.Met42Leu, may similarly disrupt protein function. The p.Met42Leu variant is located in a region where other pathogenic and likely pathogenic variants have been described without benign variation. Pathogenic and likely pathogenic variants have been described in this region and disrupt the function of GLA, resulting in reduced or absent alpha-galactosidase A enzyme activity. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Met42Leu variant as pathogenic for X-linked Fabry disease based on the information above. [ACMG evidence codes used: PS3; PM1; PM2; PM5; PP4]