rs200586324

chr17-80104852-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2 PM5 PP3 PP5_Strong

The NM_000152.5(GAA):c.266G>A(p.Arg89His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,612,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R89C) has been classified as Uncertain significance.

• 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 Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-80104852-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2754338.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.84
• PP5: Variant 17-80104852-G-A is Pathogenic according to our data. Variant chr17-80104852-G-A is described in ClinVar as [Uncertain_significance]. Clinvar id is 283219.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=11, Pathogenic=2}. Variant chr17-80104852-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8	c.266G>A	p.Arg89His	missense_variant	2/20	1	NM_000152.5	P1

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

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	Centogene AG - the Rare Disease Company	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
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). -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 29, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	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. -
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, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Dec 02, 2021	The NM_000152.5(GAA):c.266G>A variant in GAA is a missense variant predicted to cause substitution of arginine by histidine at amino acid 89 (p.Arg89His). This variant has a minor allele frequency in gnomAD is 0.00016 in the South Asian population, which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion. REVEL score = 0.819 which is higher than the LSD VCEP threshold for PP3 (>0.7) and therefore meets this criterion. This variant was found in compound heterozygosity (phase unknown) with a unique pathogenic variant in GAA in 1 patient with Pompe disease (PMID: 28196920). Additional cases, both homozygous and compound heterozygous (PMID: 28600779, 25626711, 33202836) have been reported but were not included because it was not clear if they had a second P/LP variant or if they had Pompe disease. At least 4 patients with this variant had documented GAA deficiency with activity in the affected range in muscle, cultured skin fibroblasts, leukocytes, lymphocytes, whole blood or dried blood spot ( PMID: 33202836, 28196920) or were noted to have deficient GAA activity but results were not provided and were reported to be on enzyme replacement therapy for Pompe disease ( PMID: 25626711). (PP4_Moderate). Based on the ClinGen LSD VCEP's specifications, this data meets PP4_Moderate and PM3_Supporting. 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. This meets the ClinGen LSD VCEP specifications for BS3_Supporting. There is a ClinVar entry for this variant (Variation ID: 283219; 1 star review status) with 6 submitters classifying the variant as a variant of uncertain significance and 2 as pathogenic. In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for Pompe disease. ACMG/AMP criteria met, based on the specification of the ClinGen LSD VCEP: PP4_Moderate, PP3, PM2_Supporting, PM3_Supporting, BS3_Supporting. -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Nov 09, 2022	- -

not provided Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Sep 13, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 22, 2022	PP3, PP4, PM2 -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Dec 02, 2021	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 (Kroos M et al., 2012); 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 (Monies D et al., 2017); Reported in additional patients with GSDII with either a variant of uncertain significance in trans or for whom a second variant was not identified (Hahn A et al., 2015; Nair P et al., 2018; Bertoli-Avella AM et al., 2021); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Reported in ClinVar (ClinVar Variant ID# 283219; ClinVar); This variant is associated with the following publications: (PMID: 25626711, 30293248, 31342611, 33202836, 32860008, 22644586, 27927596, 28600779, 34426522, 34602496) -
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	Revvity Omics, Revvity	Oct 26, 2023	- -

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
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.63	T
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;