X-101398468-G-C

Position:

• chrX-101398468-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 9P and 4B. PM1 PM5 PP3_Strong PP5 BS2

The NM_000169.3(GLA):​c.901C>G​(p.Arg301Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000458 in 1,091,099 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R301Q) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0000046 (0 hom. 2 hem.)
• Consequence: GLA NM_000169.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:1
• Conservation: PhyloP100: 1.43

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 5 ACMG points.

• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_000169.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-101398467-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 10715.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant X-101398468-G-C is Pathogenic according to our data. Variant chrX-101398468-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 179546.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=5, Uncertain_significance=1}. Variant chrX-101398468-G-C is described in Lovd as [Pathogenic].
• BS2: High Hemizygotes in GnomAdExome4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLA	NM_000169.3	c.901C>G	p.Arg301Gly	missense_variant	6/7	ENST00000218516.4
RPL36A-HNRNPH2	NM_001199973.2	c.300+3011G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLA	ENST00000218516.4	c.901C>G	p.Arg301Gly	missense_variant	6/7	1	NM_000169.3	P1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.00000458 AC: 5 AN: 1091099 Hom.: 0 Cov.: 30 AF XY: 0.00000561 AC XY: 2 AN XY: 356769

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000598

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Fabry disease Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 24, 2021	Variant summary: GLA c.901C>G (p.Arg301Gly) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 183457 control chromosomes. c.901C>G has been reported in the literature in multiple individuals affected with Fabry Disease, and in some patients specifically with reported Anderson-Fabry disease (Calcagnino_2011, Romani_2015, Liguori_2017, Shabeer_2002, Spinelli_2020). These data indicate that the variant is very likely to be associated with disease. Experimental studies have shown the variant to have reduced alpha-Gal activity in vitro: enzyme activity was 19.3% of wild-type, which increased to 56.5% with the addition of Migalastat (Lukas_2013); similarly the variant was reported with in vitro activity of 19.1% of wild-type, which increased to 64.7% of with the addition of Migalastat (Benjamin_2016). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 12, 2024	This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 301 of the GLA protein (p.Arg301Gly). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Fabry disease (PMID: 12175777, 28672034; Invitae). ClinVar contains an entry for this variant (Variation ID: 179546). 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 have shown that this missense change affects GLA function (PMID: 23935525, 27657681). This variant disrupts the p.Arg301 amino acid residue in GLA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 2171331, 8738659, 9395081, 11688386, 15702404, 20505683, 21598360, 22241068, 23378663). 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. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Oct 16, 2023

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 17, 2023

The p.R301G pathogenic mutation (also known as c.901C>G), located in coding exon 6 of the GLA gene, results from a C to G substitution at nucleotide position 901. The arginine at codon 301 is replaced by glycine, an amino acid with dissimilar properties. This alteration has been reported in numerous individuals with Fabry disease, having low enzyme activity observed (Shabbeer J et al. Mol Genet Metab, 2002 May;76:23-30; Calcagnino M et al. J Am Coll Cardiol, 2011 Jun;58:88-9; Romani I et al. J Stroke Cerebrovasc Dis, 2015 Nov;24:2588-95; Esposito R et al. Eur Heart J Cardiovasc Imaging, 2019 Apr;20:438-445; Citro R et al. Front Cardiovasc Med, 2022 Apr;9:838200; Di Risi T et al. Int J Mol Sci, 2022 Oct;23:[ePub ahead of print]). Another alteration at the same codon, p.R301Q (c.902G>A), has been detected in individuals with Fabry disease, who had reduced enzyme activity (Sakuraba H et al. Am J Hum Genet. 1990;47:784-789; Shin SH et al Biochem. Biophys. Res. Commun. 2007 Jul;359(1):168-73; Sawada K et al. Clin. Nephrol. 1996 May;45:289-294). In vitro studies showed this alteration impacts protein function (Lukas J et al. PLoS Genet, 2013 Aug;9:e1003632; Benjamin ER et al. Genet Med, 2017 Apr;19:430-438). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Feb 14, 2014

Variant classified as Uncertain Significance - Favor Pathogenic. The Arg301Gly v ariant in GLA has been listed in HGMD as reported in an individual with Fabry di sease, though that publication could not be found. Studies have shown that this variant leads to reduce, but residual GLA function (Lukas 2013); however, this i n vitro assay may not accurately represent biological function. This variant was absent from large population studies. Other missense variants at this position (Arg301Gln, Arg301Pro) have been reported in individuals with Fabry disease (Sak uraba 1990, Ashley 2001), suggesting that variation at this position may not be tolerated, though additional studies are needed. Computational prediction tools and conservation analysis suggest that the Arg301Gly variant may impact the prot ein, though this information is not predictive enough to determine pathogenicity . Although this data supports that this variant may be pathogenic, additional st udies are needed to fully assess its clinical significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.52
CardioboostCm	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.65	D
BayesDel_noAF	Pathogenic	0.69
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	D;.
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Pathogenic	0.98	D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	H;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.65	T
PROVEAN	Pathogenic	-6.7	D;.
REVEL	Pathogenic	0.92
Sift	Uncertain	0.020	D;.
Sift4G	Uncertain	0.017	D;.
Polyphen		1.0	D;.
Vest4		0.97
MutPred		0.90		Loss of solvent accessibility (P = 0.0509);.;
MVP		1.0
MPC		2.0
ClinPred		1.0	D
GERP RS		3.0
Varity_R		0.96
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs398123224; hg19: chrX-100653456;