rs782722577

Positions:

• chrX-101403933-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1 BS2

The NM_000169.3(GLA):​c.247G>A​(p.Asp83Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000373 in 1,207,559 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D83D) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 1 hem., cov: 23)
  • Exomes 𝑓: 0.000040 (0 hom. 12 hem.)
• Consequence: GLA NM_000169.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:10 B:1
• Conservation: PhyloP100: 3.38

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 Likely_benign. Variant got -2 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 6 uncertain in NM_000169.3
• BS2: High Hemizygotes in GnomAdExome4 at 12 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLA	NM_000169.3	c.247G>A	p.Asp83Asn	missense_variant	2/7	ENST00000218516.4
RPL36A-HNRNPH2	NM_001199973.2	c.301-8003C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLA	ENST00000218516.4	c.247G>A	p.Asp83Asn	missense_variant	2/7	1	NM_000169.3	P1

Frequencies

GnomAD3 genomes AF: 0.00000888 AC: 1 AN: 112649 Hom.: 0 Cov.: 23 AF XY: 0.0000287 AC XY: 1 AN XY: 34795

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000187

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000218 AC: 4 AN: 183388 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 67824

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: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000489

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000402 AC: 44 AN: 1094910 Hom.: 0 Cov.: 29 AF XY: 0.0000333 AC XY: 12 AN XY: 360392

Gnomad4 AFR exome AF: 0.0000380

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: 0.0000512

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000888 AC: 1 AN: 112649 Hom.: 0 Cov.: 23 AF XY: 0.0000287 AC XY: 1 AN XY: 34795

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000187

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000868 Hom.: 0

Bravo AF: 0.00000756

ExAC AF: 0.0000165 AC: 2

EpiCase AF: 0.000109

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:10 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Fabry disease Uncertain:6

Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Sep 01, 2022	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 83 of the GLA protein (p.Asp83Asn). This variant is present in population databases (rs782722577, gnomAD 0.005%). This missense change has been observed in individual(s) with reduced alpha-galactosidase activity on screening tests and/or individuals affected with stroke (PMID: 23306324, 23935525, 24365053, 26070511). This missense change has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (PMID: 26070511). ClinVar contains an entry for this variant (Variation ID: 222202). 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: "Benign"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GLA function (PMID: 27657681). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 16, 2023	This missense variant replaces aspartic acid with asparagine at codon 83 of the GLA protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function. A functional study has shown that this variant results in slightly reduced GLA enzyme activity (PMID: 27657681). This variant has been reported in two female affected with heart diseases (PMID: 24496231, 29227985), two individuals affected with stroke (PMID: 23306324, 23935525, 26070511), and in one female affected with kidney disease (PMID: 24365053). GLA enzyme activity or Gb3 levels were reported to be normal in some of these patients (PMID: 24496231, 26070511, 29227985), as well as abnormal in a few others (PMID: 23306324, 24365053). This variant has also been reported in hemizygous state in one patient's brother, who showed no manifestations of Fabry disease, and had normal plasma and leukocyte GAL enzyme activities (PMID: 26070511). This variant has been identified in 4/183388 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. -
Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 13, 2023	This missense variant replaces aspartic acid with asparagine at codon 83 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). A functional study has shown that this variant results in slightly reduced GLA enzyme activity (PMID: 27657681). This variant has been reported in two individuals affected with heart diseases (PMID: 24496231, 29227985), two individuals affected with stroke (PMID: 23306324, 23935525, 26070511), and in one female affected with kidney disease (PMID: 24365053). GLA enzyme activity or Gb3 levels were reported to be normal in some of these patients (PMID: 24496231, 26070511, 29227985), as well as abnormal in a few others (PMID: 23306324, 24365053). This variant has also been reported in hemizygous state in one patient's brother, who showed no manifestations of Fabry disease, and had normal plasma and leukocyte GAL enzyme activities (PMID: 26070511). This variant has been identified in 4/183388 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. -

not provided Uncertain:3 Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 14, 2016	- -
Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Sep 22, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 28, 2019	See Variant Classification Assertion Criteria. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 22, 2022

The p.D83N variant (also known as c.247G>A), located in coding exon 2 of the GLA gene, results from a G to A substitution at nucleotide position 247. The aspartic acid at codon 83 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been identified in cohorts of subjects with stroke, heart disease and kidney disease (Lukas J et al. PLoS Genet., 2013 Aug;9:e1003632; Herrera J et al. Clin. Nephrol., 2014 Feb;81:112-20; Ferreira S et al. Clin. Chim. Acta, 2015 Jul;447:96-104; Schiffmann R et al. Genet. Med., 2018 07;20:754-759). One female subject with stroke was noted to carry this alteration, but the alteration was also noted in her unaffected brother (Ferreira S et al. Clin. Chim. Acta, 2015 Jul;447:96-104). Based on data from gnomAD, the A allele has an overall frequency of 0.0022% (4/183388) total alleles studied, with 0 hemizygote(s) observed. The highest observed frequency was 0.0049% (4/81872) of European (non-Finnish) alleles. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
CardioboostCm	Uncertain	0.65
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.91	D;.
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Pathogenic	0.99	D;D
M_CAP	Pathogenic	0.91	D
MetaRNN	Uncertain	0.47	T;T
MetaSVM	Pathogenic	0.87	D
MutationAssessor	Uncertain	2.4	M;.
MutationTaster	Benign	1.0	D
PrimateAI	Benign	0.34	T
PROVEAN	Uncertain	-2.4	N;.
REVEL	Uncertain	0.64
Sift	Uncertain	0.018	D;.
Sift4G	Uncertain	0.018	D;.
Polyphen		0.98	D;.
Vest4		0.20
MVP		0.99
MPC		0.79
ClinPred		0.34	T
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.84
gMVP		0.92

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: rs782722577; hg19: chrX-100658921;