rs200586324

Positions:

• chr17-80104852-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM2_Supporting BS3_Supporting PP4_Moderate PM3 PP3

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.266G>A variant in GAA is a missense variant predicted to cause substitution of arginine by histidine at amino acid 89 (p.Arg89His). Two individuals with this variant have been reported to exhibit clinical symptoms of infantile onset Pompe disease, one of them on enzyme replacement therapy (PMID:22644586 25626711) (PP4_Moderate). One of them is homozygous for c.[266G>A, 546+45G>C] (PMID:22644586), and the other is compound heterozygous for c.266G>A and c.104T>C (p.Phe35Ser) (PMID:25626711). The clinical significance of c.[266G>A, 546+45G>C] and c.104T>C (p.Phe35Ser) is unknown. The variant was also found in compound heterozygosity with c.2237G>C (p.Trp746Ser) (LP based on classification by the ClinGen Lysosomal Diseases VCEP) by exome sequencing in a proband, confirmed in trans; three siblings have the same genotype. Three of the siblings have GAA activity consistent with late onset disease, and GAA activity was slightly above this range in the remaining sibling. However, none of them have developed clinical symptoms of Pompe disease yet (see ClinVar Variation ID: 283219; SCV003927052.1). Individuals identified by newborn screen, and so far clinically asymptomatic, have the genotype c.-32-13T>G/c.266G>A; c.1377C>G (PMID:33202836); or are compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen LD VCEP, either c.1655T>C (p.Leu552Pro) (PMID:33202836) or c.525delT (PMID:28196920). Another individual, with dual molecular diagnoses of GSD 1, and Pompe is homozygous for c.266G>A (p.Arg89His) but no clinical details are available (PMID:28600779). Therefore, without reports of any symptomatic individuals who have this variant in trans with a variant that has been classified as pathogenic or likely pathogenic by the ClinGen LD VCEP, PM3 is not met at the current time. The highest population minor allele frequency in gnomAD v2.1.1 is 0.001168 in the Ashkenazi Jewish population (12/10272; no homozygotes). The highest population minor allele frequency in a continental population in gnomAD v2.1.1. is 0.00016 (5/30550) in the South Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion. The computational predictor REVEL gives a score of 0.819 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). When expressed in COS cells, this variant was classified as Class E ("presumably nonpathogenic") by Kroos et al, 2012 (PMID:22644586). This includes 43.5% GAA activity in cells and 20% in medium, and is normally synthesized (though less than normal) and processed on Western blot (BS3_Supporting). Three other missense variants at the same position have been reported - c.265C>T (p.Arg89Cys) (VUS based on classification by the ClinGen LD VCEP; ClinVar Variation ID: 456412, SCV002817439.1), c.265C>A (p.Arg89Ser) (ClinVar Variation ID: 1989151), and c.266G>T (p.Arg89Leu) (ClinVar Variation ID: 2754338) (not yet classified by the ClinGen LD VCEP).There is a ClinVar entry for this variant (Variation ID: 283219). In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for Pompe disease. GAA-specific ACMG/AMP criteria met, based on the specification of the ClinGen Lysosomal Diseases VCEP: PP4_Moderate, PP3, PM2_Supporting, BS3_Supporting.(Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on April 16, 2024). LINK:https://erepo.genome.network/evrepo/ui/classification/CA8814833/MONDO:0009290/010

• Frequency:
  • Genomes: 𝑓 0.000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00010 (1 hom.)
• Consequence: GAA NM_000152.5 missense
• Clinical Significance: Uncertain significance reviewed by expert panel P:4 U:12
• Conservation: PhyloP100: 9.79

Genes affected

GAA (HGNC:4065): (alpha glucosidase) This gene encodes lysosomal alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes. The encoded preproprotein is proteolytically processed to generate multiple intermediate forms and the mature form of the enzyme. Defects in this gene are the cause of glycogen storage disease II, also known as Pompe's disease, which is an autosomal recessive disorder with a broad clinical spectrum. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.
• BS3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAA	NM_000152.5	c.266G>A	p.Arg89His	missense_variant	2/20	ENST00000302262.8	NP_000143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAA	ENST00000302262.8	c.266G>A	p.Arg89His	missense_variant	2/20	1	NM_000152.5	ENSP00000305692.3

Frequencies

GnomAD3 genomes AF: 0.0000657 AC: 10 AN: 152196 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000141 AC: 35 AN: 248182 Hom.: 0 AF XY: 0.000148 AC XY: 20 AN XY: 134808

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000290

Gnomad ASJ exome AF: 0.00120

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000164

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000134

Gnomad OTH exome AF: 0.000330

GnomAD4 exome AF: 0.000105 AC: 153 AN: 1460536 Hom.: 1 Cov.: 31 AF XY: 0.000110 AC XY: 80 AN XY: 726566

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.000957

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000139

Gnomad4 FIN exome AF: 0.0000191

Gnomad4 NFE exome AF: 0.0000782

Gnomad4 OTH exome AF: 0.000282

GnomAD4 genome AF: 0.0000657 AC: 10 AN: 152196 Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7 AN XY: 74348

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000118

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000231 Hom.: 0

Bravo AF: 0.000147

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.0000742 AC: 9

EpiCase AF: 0.000273

EpiControl AF: 0.000119

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:4 Uncertain:12

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:4 Uncertain:6

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Uncertain significance, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Apr 16, 2024	The NM_000152.5:c.266G>A variant in GAA is a missense variant predicted to cause substitution of arginine by histidine at amino acid 89 (p.Arg89His). Two individuals with this variant have been reported to exhibit clinical symptoms of infantile onset Pompe disease, one of them on enzyme replacement therapy (PMID: 22644586 25626711) (PP4_Moderate). One of them is homozygous for c.[266G>A, 546+45G>C] (PMID: 22644586), and the other is compound heterozygous for c.266G>A and c.104T>C (p.Phe35Ser) (PMID: 25626711). The clinical significance of c.[266G>A, 546+45G>C] and c.104T>C (p.Phe35Ser) is unknown. The variant was also found in compound heterozygosity with c.2237G>C (p.Trp746Ser) (LP based on classification by the ClinGen Lysosomal Diseases VCEP) by exome sequencing in a proband, confirmed in trans; three siblings have the same genotype. Three of the siblings have GAA activity consistent with late onset disease, and GAA activity was slightly above this range in the remaining sibling. However, none of them have developed clinical symptoms of Pompe disease yet (see ClinVar Variation ID: 283219; SCV003927052.1). Individuals identified by newborn screen, and so far clinically asymptomatic, have the genotype c.-32-13T>G/c.266G>A; c.1377C>G (PMID: 33202836); or are compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen LD VCEP, either c.1655T>C (p.Leu552Pro) (PMID: 33202836) or c.525delT (PMID: 28196920). Another individual, with dual molecular diagnoses of GSD 1, and Pompe is homozygous for c.266G>A (p.Arg89His) but no clinical details are available (PMID: 28600779). Therefore, without reports of any symptomatic individuals who have this variant in trans with a variant that has been classified as pathogenic or likely pathogenic by the ClinGen LD VCEP, PM3 is not met at the current time. The highest population minor allele frequency in gnomAD v2.1.1 is 0.001168 in the Ashkenazi Jewish population (12/10272; no homozygotes). The highest population minor allele frequency in a continental population in gnomAD v2.1.1. is 0.00016 (5/30550) in the South Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion. The computational predictor REVEL gives a score of 0.819 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). When expressed in COS cells, this variant was classified as Class E ("presumably nonpathogenic") by Kroos et al, 2012 (PMID:22644586). This includes 43.5% GAA activity in cells and 20% in medium, and is normally synthesized (though less than normal) and processed on Western blot (BS3_Supporting). Three other missense variants at the same position have been reported - c.265C>T (p.Arg89Cys) (VUS based on classification by the ClinGen LD VCEP; ClinVar Variation ID: 456412, SCV002817439.1), c.265C>A (p.Arg89Ser) (ClinVar Variation ID: 1989151), and c.266G>T (p.Arg89Leu) (ClinVar Variation ID: 2754338) (not yet classified by the ClinGen LD VCEP).There is a ClinVar entry for this variant (Variation ID: 283219). In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for Pompe disease. GAA-specific ACMG/AMP criteria met, based on the specification of the ClinGen Lysosomal Diseases VCEP: PP4_Moderate, PP3, PM2_Supporting, BS3_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on April 16, 2024). -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 18, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 29, 2024	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Arg89His variant in GAA has been reported in 3 individuals with Glycogen Storage Disease II (PMID: 22644586, 28600779, 25626711), but it is unclear whether this variant causes Glycogen Storage Disease II. This variant has also been reported as a VUS by Invitae and EGL Genetic Diagnostics in ClinVar (Variation ID: 283219), and has been identified in 0.117% (12/10272) of Ashkenazi Jewish chromosomes, 0.016% (5/30550) of South Asian chromosomes, and 0.015% (19/127034) of European (Non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs200586324). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. One individual was homozygous for this variant and another reported pathogenic variant for Glycogen Storage Disease I in G6PC, p.Arg83Cys (PMID: 28600779; Variation ID: 11998). Another individual was homozygous for this variant and another VUS reported in the literature, c.546+45G>C (PMID: 22644586). This variant was also seen in trans with a rare VUS in GAA (PMID: 25626711). In vitro functional studies provide some evidence that the p.Arg89His variant may not impact protein function (PMID: 22644586). 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. In summary, while the clinical significance of the p.Arg89His variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP Criteria applied: PP3, BS3_Supporting, BP2 (Richards 2015). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Biochemical Genetics Department, Cyprus Institute of Neurology and Genetics	May 05, 2023	The classification of the variant was performed according to the recommendations of ClinGen lysosomal storage disorders variant curation expert panel (Guidelines version 2, specific for the GAA gene). The NM_000152.5(GAA):c.266G>A p.(Arg89His) variant is a missense variant that replaces a highly conserved arginine residue (Arg89) by histidine (p.Arg89His). This variant is present at an extremely low frequency in gnomAD databases (ƒExomes = 0.0000141, ƒgenomes = 0.0000657), only in heterozygosity and meets the PM2_Supporting criterion (1pt). The c.266G>A variant confirmed to be in trans with the pathogenic variant NM_000152.5:c.2237G>C p.(Trp746Ser) in our case. Moreover, it has been identified in compound heterozygosity with the c.546+45G>C variant in individuals with clinical features of Pompe disease [PMID: 22644586], thus meets the PM3_strong criterion (2pts). The REVEL score is 0.819 which is higher than the LSD VCEP threshold for PP3 (>0.7) and therefore meets this criterion (1pt). An alternative variant NM_000152.5(GAA):c.265C>A (p.Arg89Ser) is classified as Likely Pathogenic [1 star, ClinVar, PM5_supporting (1pt)]. The four individuals, with the c.[266G>A];[2237G>C] genotype (2-13years), were found to have GAA activity clearly within the patient range (1.1-4.9nmol/h/mg) in leukocytes using 4-methylumbelliferyl-α-D-glucoside as a substrate. Using glycogen as a substrate, the GAA activity was found to be within the range for LOPD patients (3-10nmol/h/mg) for one subject and slightly above the upper limit for the three subjects. The presence of the KM-mutant polymorphism c.271G>A and the pseudodeficiency variant c.[1726G>A (p.Gly576Ser); 2065G>A (p.Glu689Lys)] was excluded. Based on the ClinGen LSD VCEP's specifications, this data meets PP4_Moderate rule (2pts). In summary, this variant meets the criteria to be classified as a likely pathogenic variant (total 7pts) for Pompe disease. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 27, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 89 of the GAA protein (p.Arg89His). This variant is present in population databases (rs200586324, gnomAD 0.1%). This missense change has been observed in individuals with clinical features of Pompe disease (PMID: 22644586, 25626711, 32860008, 34602496; Invitae). ClinVar contains an entry for this variant (Variation ID: 283219). 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 expected to disrupt GAA protein function with a positive predictive value of 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GAA function (PMID: 22644586). For these reasons, this variant has been classified as Pathogenic. -

not provided Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 22, 2024	Reported in the homozygous state in the presence of an additional homozygous GAA variant (c.-32-13T>G, a common pathogenic variant in individuals with adult-onset GSDII) in an infant severely affected with GSDII; functional studies indicated only minimally reduced enzyme activity and the R89H variant was classified as presumably non-pathogenic by the authors (PMID: 22644586); Reported in the homozygous state in a patient with a dual diagnosis of GSDII and GSDI who also harbored a homozgyous pathogenic variant in the G6PC gene (PMID: 28600779); Reported in additional patients with GSDII with either a variant of uncertain significance in trans or for whom a second variant was not identified (PMID: 32860008, 25626711, 30293248); 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: 25626711, 30293248, 31342611, 27927596, 34426522, 34602496, Goomber2022[abstract], 33073007, 31254424, 37087815, 37600231, 32860008, 28600779, 33202836, 22644586, 19343043, 22253258) -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Sep 13, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 26, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 22, 2022	PP3, PP4, PM2 -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 09, 2022

Variant summary: GAA c.266G>A (p.Arg89His) results in a non-conservative amino acid change located in the P-type trefoil domain (IPR000519) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 248182 control chromosomes (gnomAD). It has also been reported at a frequency of 0.0016 in the Turkish population, including one homozygote whose clinical status was not specified (Kars_2021). These frequencies are not significantly higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (0.0042), allowing no conclusion about variant significance. c.266G>A has been reported in the literature in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) and also in individuals suspected of the late onset form of the disease, but without a definitive clinical diagnosis (e.g. Hahn_2015, Lin_2017, Nair_2018, Tang_2020, Ficicioglu_2020, Bertoli-Avella_2021). In these reports it has been found in the compound heterozygous state together with pathogenic variants, but also with variants of uncertain significance, and in the heterozygous state where a second allele has not been identified or not specified. Therefore these reports do not provide unequivocal conclusions about association of the variant with Pompe Disease. At least one publication reports experimental evidence evaluating an impact on protein function. It found that the variant results in 43.5% of WT activity in vitro and described the variant as presumably non-pathogenic (Kroos_2012). Nine submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. The majority classified the variant as VUS (n=7) and the other classified the variant as likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as VUS. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Pathogenic	0.17
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.71	D;.;D;D
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D;D;.;D
M_CAP	Pathogenic	0.48	D
MetaRNN	Pathogenic	0.84	D;D;D;D
MetaSVM	Uncertain	0.75	D
MutationAssessor	Pathogenic	4.3	.;.;H;H
PrimateAI	Uncertain	0.63	T
PROVEAN	Uncertain	-3.6	.;.;D;D
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0020	.;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	.;.;D;D
Vest4		0.93, 0.94
MVP		0.99
MPC		0.60
ClinPred		0.97	D
GERP RS		4.9
Varity_R		0.83
gMVP		0.86

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: rs200586324; hg19: chr17-78078651;