rs199473684

chrX-101399747-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_000169.3(GLA):c.640-801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 112,274 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: 𝑓 0.000018 (0 hom., 1 hem., cov: 23)
• Consequence: GLA NM_000169.3 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:12 U:2 O:1
• Conservation: PhyloP100: 0.201

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 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-101399747-C-T is Pathogenic according to our data. Variant chrX-101399747-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 10768.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=11, Uncertain_significance=1, not_provided=1}. Variant chrX-101399747-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLA	NM_000169.3	c.640-801G>A		intron_variant		ENST00000218516.4
RPL36A-HNRNPH2	NM_001199973.2	c.300+4290C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLA	ENST00000218516.4	c.640-801G>A		intron_variant		1	NM_000169.3	P1

Frequencies

GnomAD3 genomes AF: 0.0000178 AC: 2 AN: 112222 Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1 AN XY: 34386

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000554

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0000178 AC: 2 AN: 112274 Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1 AN XY: 34448

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000556

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000453

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:12 Uncertain:2 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Fabry disease Pathogenic:5 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 11, 2021	Variant summary: The variant c.640-801G>A is located in intron 4 of the GLA gene. Several in vitro studies demonstrated, that the variant activates a cryptic exon between exon 4 and 5 that results in the insertion of 57 intronic nucleotide, leading to a premature stop codon (Ishii 2002, Chiang 2017, Chang 2017). However, the variant had an incomplete effect on splicing, as the full length product was also detected. Though the truncated variant-protein had no enzyme activity (Ishii 2002), since the normal transcript was also present, it resulted in some residual enzyme activity in samples from male individuals carrying the variant (Ishii 2002, Lin 2010, Chien 2012, Chang 2017). The variant allele was found in 1/22077 control chromosomes in the genome dataset of gnomAD database (detected in an East Asian individual). c.640-801G>A has been reported in the literature in several individuals affected with the Cardiac Variant of Fabry Disease (FD) (e.g. Ishii 2002, Lin 2010, Hsu 2019), but was also found in controls, especially in East Asian populations, where the variant was observed with a relatively high frequency (~0.0011) in Taiwanese individuals during newborn screening and in healthy adult controls (Chien 2012, Chiang 2017). Though this frequency is higher than predicted for a pathogenic variant in the GLA gene, a recent study indicated that the variant might result in a latent disease progression, with Fabry Disease-associated late onset cardiomyopathy that in many cases can only be detected with more sensitive diagnostic methods or much later in life (Hsu 2019). These authors also suggested that the prevalence of late-onset FD might be much higher than previously expected. In addition, another recent study proposed a multifactorial model, consisting of combinations of multiple variants in conjunction with other organ-related or environmental factors as contributing to the associated cardiac complications and the natural history of disease progression related to this variant (Juang 2019). Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation; eight classified the variant as likely pathogenic/pathogenic while one classified as VUS. Based on the evidence outlined above, the variant causes a cryptic splice-mutation resulting in decreased enzyme activity, and although it is relatively common in some East Asian subpopulations, it was reported in several individuals with late-onset cardiac FD phenotype; therefore it was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 08, 2024	This variant is located in intron 4 of the GLA gene and is also known as IVS4+919G>A and c.639+919G>A based on a different transcript NM_000169.2. RNA studies have shown that this variant causes the inclusion of 57 bases from intron 4 as a pseudoexon, resulting in the expression of truncated protein (PMID: 11828341, 27595546, 28430823). These studies have shown that the alternate transcript was present at low levels in most normal tissues and is significantly increased in cells from carrier individuals affected with Fabry disease. This variant has been reported in over forty males of East Asian ancestry affected with mild, late-onset Fabry disease (PMID: 11828341, 20031620, 32246049, 36013057). This variant has also been observed in individuals affected with cardiomyopathy, who showed reduced GLA enzyme activity (PMID: 20031620, 25611685, 30731207, 31028938) and in an individual affected with left ventricular hypertrophy (PMID: 35743592). This variant has been reported to segregate with disease in multiple families affected with Fabry disease or hypertrophic cardiomyopathy (ClinVar SCV000203980.4). Literature has reported the absence of this variant in 230 unaffected control males and 149 unaffected control females (PMID: 11828341, 19621417). This variant has been identified in 1/22077 chromosomes by the Genome Aggregation Database (gnomAD; low coverage region). Large newborn screening studies have shown that this variant is highly prevalent in the Taiwanese population with up to 1/875 males and 1/399 females being carriers (PMID: 19621417, 20031620, 22437327). Mean enzyme activities in the male and female carriers were 23% and 55% of normal mean values, respectively (PMID: 22437327). Loss of GLA function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 17, 2024	This sequence change falls in intron 4 of the GLA gene. It does not directly change the encoded amino acid sequence of the GLA protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs199473684, gnomAD 0.1%). This variant has been observed in individual(s) with Fabry disease and hypertrophic cardiomyopathy (PMID: 11828341, 19621417, 20031620, 22437327, 25611685). It is commonly reported in individuals of Taiwanese ancestry (PMID: 27931613). This variant is also known as IVS4+919G>A. ClinVar contains an entry for this variant (Variation ID: 10768). Studies have shown that this variant results in insertion of 57bp pseudoexon sequence in intron 4 and introduces a premature termination codon (PMID: 11828341, 27595546, 28430823). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 15, 2023	This variant is located in intron 4 of the GLA gene and is also known as IVS4+919G>A and c.639+919G>A based on a different transcript NM_000169.2. RNA studies have shown that this variant causes the inclusion of 57 bases from intron 4 as a pseudoexon, resulting in the expression of truncated protein (PMID: 11828341, 27595546, 28430823). These studies have shown that the alternate transcript was present at low levels in most normal tissues and is significantly increased in cells from carrier individuals affected with Fabry disease. This variant has been reported in over forty males of East Asian ancestry affected with mild, late-onset Fabry disease (PMID: 11828341, 20031620, 32246049, 36013057). This variant has also been observed in individuals affected with cardiomyopathy, who showed reduced GLA enzyme activity (PMID: 20031620, 25611685, 30731207, 31028938) and in an individual affected with left ventricular hypertrophy (PMID: 35743592). This variant has been reported to segregate with disease in multiple families affected with Fabry disease or hypertrophic cardiomyopathy (ClinVar SCV000203980.4). Literature has reported the absence of this variant in 230 unaffected control males and 149 unaffected control females (PMID: 11828341, 19621417). This variant has been identified in 1/22077 chromosomes by the Genome Aggregation Database (gnomAD; low coverage region). Large newborn screening studies have shown that this variant is highly prevalent in the Taiwanese population with up to 1/875 males and 1/399 females being carriers (PMID: 19621417, 20031620, 22437327). Mean enzyme activities in the male and female carriers were 23% and 55% of normal mean values, respectively (PMID: 22437327). Loss of GLA function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The c.639+919G>A variant in GLA has been reported in at least 6 individuals with Fabry disease, segregated with disease in 3 affected relatives from 1 family (PMID:29215092, 25611685, 22437327,19621417, 20821055, 20031620,11828341), and has been identified in 0.1% (1/1000) of East Asian chromosomes, including a single hemizygote, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs199473684). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar as a VUS by OMIM and as pathogenic by the Laboratory for Molecular Medicine (Partners Healthcare), Invitae, EGL Clinical Diagnostics, and GeneReviews (ID:10768). In vitro functional studies provide some evidence that the c.639+919G>A variant may impact protein function as a result of alternative splicing and decreased enzyme activity (PMID:11828341, 28430823, 27595546). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The phenotype of an individual hemizygous for this variant is highly specific for Fabry disease based on the classic phenotype consistent with disease (PMID: 25611685, 22437327,19621417, 20821055, 20031620,11828341). In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PS3_moderate, PP1, PP4 (Richards 2015). -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Nov 30, 2020	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 15, 2021	Has been reported as a common variant in Taiwanese and Japanese populations in association with reduced GLA enzyme activity levels and Fabry late-onset cardiac phenotype (for examples, see Ishii et al., 2002; Lin et al., 2010; Chien et al., 2012; Hsu et al., 2016; Sakuraba et al., 2018; of note, this variant is also reported as c.639+919 G>A due to the use of alternate nomenclature); Has been observed in 1/1000 alleles from individuals of Asian background, including one hemizygous individual, in large population cohorts (Lek et al., 2016); In vitro functional studies have shown that c.640-801 G>A creates a cryptic splice site that causes abnormal gene splicing through introduction of an additional 57 nucleotides into the GLA transcript (Ishii et al., 2002; Palhais et al., 2016; Chang et al., 2017); Additional functional studies have shown that this variant is associated with approximately 10% residual alpha-galactosidase activity in patient lymphoblasts (Ishii et al, 2002); Reported in ClinVar as pathogenic (ClinVar Variant ID# 10768; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 33204599, 32246049, 32150461, 31447099, 30477121, 31956509, 30662066, 30666049, 30386727, 30380558, 30103270, 28082092, 29215092, 27554049, 28430823, 28377241, 20031620, 11828341, 20821055, 28322587, 27931613, 26869469, 25611685, 24980630, 19621417, 19823873, 24055776, 22437327, 27595546) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 28, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Aug 31, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 24, 2017	- -

Cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

May 03, 2023

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 14, 2022

The c.640-801G>A intronic pathogenic mutation results from a G to A substitution 801 nucleotides upstream from coding exon 5 in the GLA gene. This alteration (also referred to as IVS4+919G>A, c.936+919G>A or c.639+919G>A in the literature) has been detected in many individuals from Asian populations with reduced alpha-galactosidase A enzyme activity on newborn screen, and has also been detected in adult males and females with reduced enzyme activity reported to have late-onset, primarily cardiac variant Fabry disease with presentation typically after 40 years of age, although the frequency of this variant suggests it exhibits reduced penetrance (Ishii S et al. Am J Hum Genet. 2002;70:994-1002; Hwu WL et al. Hum Mutat. 2009;30:1397-405; Lin HY et al. Circ Cardiovasc Genet. 2009;2:450-6; Lin HY et al. J Inherit Metab Dis. 2010;33:619-24; Chien YH et al. Mol Med. 2012;18:780-4; Hsu TR et al. Orphanet J Rare Dis. 2014;9:96; Kubo T et al. J Cardiol. 2017;69:302-307; Sakuraba H et al. Mol Genet Metab Rep. 2018;17:73-79). In a study of patient-derived induced pluripotent stem cells, cardiomyocytes with this alteration recapitulated the abnormal cardiac phenotype (Chou SJ et al. Int J Cardiol. 2017;232:255-263). This alteration has been demonstrated to result in aberrant splicing, leading to increased expression of a transcript including a portion of intron 4 and the introduction of a premature stop codon (Ishii S et al. Am J Hum Genet. 2002 Apr;70:994-1002; Palhais B et al. Mol Genet Metab. 2016;119:258-269; Chang WH et al. PLoS ONE. 2017;12:e0175929). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Fabry disease;C0007194:Hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 03, 2018

The c.639+919G>A variant in GLA (also described as c.640-801G>A in the literatur e) has been reported in at least 6 individuals with a later-onset, cardiac varia nt of Fabry disease (Ishii 2002) and in many individuals with hypertrophic cardi omyopathy (HCM) or left ventricular hypertrophy (LVH), all of whom exhibited red uced GLA enzyme activity levels (Ishii 2002, Lin 2009, Lin 2010, Hsu 2016, Kubo 2017). This variant has also been identified by our laboratory in 4 Asian indivi duals with HCM or Fabry disease, and segregated with disease in 3 affected relat ives (2 with Fabry disease and 1 with reduced GLA activity). This variant has be en also been identified in 1/1041 of Asian chromosomes (a hemizygous male) by th e Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs199473684). Functional studies have shown that the c.639+919G>A variant result s in the accumulation of lamellar bodies and glycosphingolipids in induced pluri potent stem cell cardiomyocytes from a patient with Fabry disease (Chou 2017). I n addition, mRNA slicing studies have shown that this variant leads to abnormal splicing, resulting in the introduction of an additional 57 nucleotides into the GLA transcript, ultimately leading to a truncated protein (Ischii 2002, Palhais 2016, Chang 2017). In summary, the c.639+919G>A variant meets criteria to be cl assified as pathogenic for Fabry disease in an X-linked manner based upon presen ce in multiple affected individuals, functional and segregation studies. ACMG/AM P Criteria applied (Richards 2015): PS3; PS4; PP1. -

Fabry disease, cardiac variant Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Apr 01, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	16
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.30		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.30		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs199473684; hg19: chrX-100654735;