chrX-101398044-G-C

Position:

• chrX-101398044-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1 PP3_Moderate BS2

The NM_000169.3(GLA):​c.1055C>G​(p.Ala352Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000364 in 1,097,447 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.0000036 (0 hom. 2 hem.)
• Consequence: GLA NM_000169.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:9 O:1
• Conservation: PhyloP100: 9.26

Genes affected

GLA (HGNC:4296): (galactosidase alpha) This gene encodes a homodimeric glycoprotein that hydrolyses the terminal alpha-galactosyl moieties from glycolipids and glycoproteins. This enzyme predominantly hydrolyzes ceramide trihexoside, and it can catalyze the hydrolysis of melibiose into galactose and glucose. A variety of mutations in this gene affect the synthesis, processing, and stability of this enzyme, which causes Fabry disease, a rare lysosomal storage disorder that results from a failure to catabolize alpha-D-galactosyl glycolipid moieties. [provided by RefSeq, Jul 2008]

RPL36A-HNRNPH2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 8 uncertain in NM_000169.3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.855
• BS2: High Hemizygotes in GnomAdExome4 at 2 Mitochondrial gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLA	NM_000169.3	c.1055C>G	p.Ala352Gly	missense_variant	7/7	ENST00000218516.4
RPL36A-HNRNPH2	NM_001199973.2	c.300+2587G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLA	ENST00000218516.4	c.1055C>G	p.Ala352Gly	missense_variant	7/7	1	NM_000169.3	P1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD3 exomes AF: 0.00000546 AC: 1 AN: 183231 Hom.: 0 AF XY: 0.0000148 AC XY: 1 AN XY: 67701

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000524

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000364 AC: 4 AN: 1097447 Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 2 AN XY: 362811

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000370

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 24

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:9 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Fabry disease Pathogenic:2 Uncertain:5

Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Ala352Gly variant in GLA has not been previously reported in individuals with Fabry disease but has been identified in 0.0052% (1/19077) of South Asian chromosomes by the Genome Aggregation Database, including 1 hemizygote (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs869312162). Although this variant has been seen in the general population, its frequency is low enough to be consistent with Fabry disease. Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. This variant has been reported in ClinVar as Likely Pathogenic by Sonic Healthcare and as a VUS by the Laboratory for Molecular Medicine and the Albrecht-Kossel-Institute (Variation ID:217410). In vitro functional studies provide some evidence that the p.Ala352Gly variant may not impact protein function (PMID: 26415523). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Ala352Gly variant is uncertain. ACMG/AMP Criteria applied: PM2_supporting, BS3_supporting, PM4 (Richards 2015). -
Uncertain significance, no assertion criteria provided	research	Albrecht-Kossel-Institute, Medical University Rostock	Jan 01, 2014	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	May 17, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 20, 2022	This missense variant replaces alanine with glycine at codon 352 of the GLA protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools are inconclusive regarding the impact of this variant on RNA splicing. Functional studies support that this variant may not have a significant impact on GLA enzyme activity (PMID: 26415523). This variant has been reported in females affected with Fabry disease (PMID: 32789421). It has also been reported in individuals with suspected but not confirmed Fabry disease (PMID: 26415523, 31860127). This variant has been identified in 1/183231 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 352 of the GLA protein (p.Ala352Gly). This variant is present in population databases (no rsID available, gnomAD 0.005%). This missense change has been observed in individuals with Fabry disease (PMID: 32789421). ClinVar contains an entry for this variant (Variation ID: 217410). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GLA protein function with a negative predictive value of 80%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GLA function (PMID: 26415523). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant disrupts the p.Ala352 amino acid residue in GLA. Other variant(s) that disrupt this residue have been observed in individuals with GLA-related conditions (PMID: 12920095, 33016649), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 27, 2023	Variant summary: GLA c.1055C>G (p.Ala352Gly) results in a non-conservative amino acid change located in the Alpha galactosidase A, C-terminal beta-sandwich domain (IPR035373) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.5e-06 in 183231 control chromosomes. c.1055C>G has been reported in the literature in at-least three unrelated females with end stage renal disease (ESRD) but not any other classic features of Fabry Disease (example, Alhemyadi_2020) and in at-least one individual with a reportedly non-definitive diagnosis of Fabry Disease (example, Balendran_2019). At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in approximately 54% of normal activity in-vitro (example, Lukas_2016). The following publications have been ascertained in the context of this evaluation (PMID: 26415523, 27916943, 31860127, 32789421, 34679477). Eight ClinVar submitters have submitted clinical-significance assessments for this variant to ClinVar after 2014, scoring the variant as uncertain significance (n=7) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 28, 2019	The p.Ala352Gly variant in GLA has not been previously reported in individuals with clinical features of Fabry disease, but was reported in two individuals with unreported clinical status who were tested for Fabry disease (Lukas 2016). It was also identified in 1/19077 South Asian chromosomes by gnomAD (https://gnomad.broadinstitute.org/) and has been reported in ClinVar (Variation ID #217410). In vitro studies suggest that that this variant has a mild reduction in enzymatic activity (Lukas 2016), but these assays may not accurately represent biological function. Computational prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Ala352Gly variant is uncertain. -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 22, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 13, 2020	Reported in patients referred for evaluation of Fabry disease and in patients with unexplained end-stage renal failure (Lukas et al., 2016; Balendran et al., 2020; Alhemyadi et al., 2020); Reported in ClinVar (ClinVar Variant ID# 217410; Landrum et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies using HEK293 cells demonstrate a high residual enzyme activity (Lukas et al., 2016); This variant is associated with the following publications: (PMID: 26415523, 32789421, 31860127) -

Migalastat response Other:1

drug response, no assertion criteria provided

research

Albrecht-Kossel-Institute, Medical University Rostock

Jan 01, 2014

- Pharmacological Chaperone response: no

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
CardioboostCm	Uncertain	0.38
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	0.13
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Pathogenic	0.92	D;.
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.64	T;T
M_CAP	Pathogenic	0.92	D
MetaRNN	Pathogenic	0.85	D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.8	M;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.55	T
PROVEAN	Uncertain	-3.1	D;.
REVEL	Pathogenic	0.66
Sift	Benign	0.10	T;.
Sift4G	Benign	0.11	T;.
Polyphen		0.98	D;.
Vest4		0.65
MutPred		0.55		Loss of stability (P = 0.1602);.;
MVP		0.92
MPC		1.5
ClinPred		0.70	D
GERP RS		4.8
Varity_R		0.78
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs869312162; hg19: chrX-100653032;