17-80104857-G-A

Position:

• chr17-80104857-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BA1 BP4

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.271G>A missense variant in GAA (p.Asp91Asn) has a highest population minor allele frequency in gnomAD v2.1.1 of 0.03291 (4183/127102 alleles; 70 homozygotes) in the European non-Finnish population, which is higher than the ClinGen LSD VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.396 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAA function. In addition, the computational splice predictors SpliceAI and varSEAK predict that the variant has no impact on splicing (BP4). This variant is frequently described as a “pseudodeficiency” variant in the literature. It has been identified as the amino acid substitution responsible for the GAA*2 alloenzyme (also known as GAA2) (PMID:2203258). GAA*2 was identified by its faster migration on starch gel electrophoresis compared to the GAA*1 alloenzyme (PMID:2688539). In addition, compared to GAA*1, GAA*2 has a 10 fold higher Km for glycogen, but similar Km for maltose and 4-MUG (PMID:2688539). No differences between the processing of GAA*2 and GAA*1 were noted on Western blot of protein from fibroblasts homozygous for either alloenzyme (PMID:2688539). Furthermore, comparable amounts of glycogen were found in the lysosomes of the GAA*1 and GAA*2 homozygous cell lines, and there was no evidence of abnormal lysosomal glycogen storage in GAA*2 fibroblasts on electron microscopy (PMID:2688539). When expressed in SV40-transformed GAA-deficient fibroblasts, c.271G>A (p.Asp91Asn) has similar GAA activity to wild type when 4-MUG is used as the substrate (PMID:2203258). Studies in cells from patients show a difference in GAA activity depending on the substrate used. In cells from individuals who are homozygous, or compound heterozygous for the variant and a known pathogenic GAA variant, false positives arose when glycogen was used as the substrate in the leukocyte assay, while the expected result was obtained when 4-MUG was used as the substrate in either the leukocyte or fibroblast assays (PMID:19387865, 33162552). Evidence from the crystal structures of native and recombinant GAA indicate that Asp91 is involved in a sugar binding site, which could explain why this variant binds carbohydrate less effectively (PMID:29061980; https://www.biorxiv.org/content/10.1101/212837v1 ). In addition, while the computational splice site predictors SpliceAI and varSEAK predict no impact on splicing, a mini-gene assay indicated that the variant results in exon 2 exclusion in about 30% of transcripts (PMID:31301153). As an explanation for how the biochemical features of this variant result in no clinical features, substrate concentrations are usually far below that required for saturation of the enzyme. A reduction in enzyme activity brought about by decrease in Vmax, or increase in Km, would be compensated for by an increase in substrate concentration, restoring the normal turnover rate and establishing an equilibrium substrate concentration (PMID:2688539).In patients with Pompe disease, c.271G>A has been found in cis with other variants that have been classified as pathogenic by the ClinGen LSD VCEP, p.Cys103Gly (PMID:16838077, 33073003) and c.877G>A (p.Gly293Arg) (PMID:27189384).There is a ClinVar entry for this variant (Variation ID: 4020) with eight submitters classifying the variant as benign, two as likely benign, and two as “other”. In summary, based on the evidence available to date, this variant meets the criteria to be classified as benign for Pompe disease. However, it is important to note that GAA activity may be in the patient range in individuals who are homozygous for the variant, or compound heterozygous for the variant and a pathogenic GAA variant, if glycogen is used as a substrate. Careful evaluation and use of 4-MUG as the substrate is necessary to provide accurate results. Therefore, this variant is classified as “other” to ensure that an explanation for deficient enzyme activity in the context of a clinically benign variant is highlighted. GAA-specific ACMG-AMP criteria applied, as specified by the ClinGen LSD VCEP: BA1. LINK:https://erepo.genome.network/evrepo/ui/classification/CA116586/MONDO:0009290/010

• Frequency:
  • Genomes: 𝑓 0.021 (61 hom., cov: 32)
  • Exomes 𝑓: 0.029 (746 hom.)
• Consequence: GAA NM_000152.5 missense
• Clinical Significance: Benign/Likely benign; other criteria provided, multiple submitters, no conflicts B:11 O:5
• 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 Benign. Variant got -9 ACMG points.

• BP4: For more information check the summary or visit ClinGen Evidence Repository.
• BA1: 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.271G>A	p.Asp91Asn	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.271G>A	p.Asp91Asn	missense_variant	2/20	1	NM_000152.5	ENSP00000305692.3

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3261 AN: 152192 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00634

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0206

GnomAD3 exomes AF: 0.0203 AC: 5048 AN: 248310 Hom.: 79 AF XY: 0.0201 AC XY: 2711 AN XY: 134866

Gnomad AFR exome AF: 0.00613

Gnomad AMR exome AF: 0.0118

Gnomad ASJ exome AF: 0.0138

Gnomad EAS exome AF: 0.000164

Gnomad SAS exome AF: 0.00809

Gnomad FIN exome AF: 0.0178

Gnomad NFE exome AF: 0.0326

Gnomad OTH exome AF: 0.0218

GnomAD4 exome AF: 0.0290 AC: 42319 AN: 1460562 Hom.: 746 Cov.: 31 AF XY: 0.0284 AC XY: 20654 AN XY: 726596

Gnomad4 AFR exome AF: 0.00439

Gnomad4 AMR exome AF: 0.0125

Gnomad4 ASJ exome AF: 0.0144

Gnomad4 EAS exome AF: 0.000126

Gnomad4 SAS exome AF: 0.00811

Gnomad4 FIN exome AF: 0.0179

Gnomad4 NFE exome AF: 0.0343

Gnomad4 OTH exome AF: 0.0234

GnomAD4 genome AF: 0.0214 AC: 3260 AN: 152310 Hom.: 61 Cov.: 32 AF XY: 0.0204 AC XY: 1519 AN XY: 74470

Gnomad4 AFR AF: 0.00633

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00932

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.0343

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0296 Hom.: 72

Bravo AF: 0.0203

TwinsUK AF: 0.0245 AC: 91

ALSPAC AF: 0.0306 AC: 118

ESP6500AA AF: 0.00658 AC: 29

ESP6500EA AF: 0.0315 AC: 271

ExAC AF: 0.0204 AC: 2476

Asia WGS AF: 0.00462 AC: 16 AN: 3478

EpiCase AF: 0.0319

EpiControl AF: 0.0307

ClinVar

Significance: Benign/Likely benign; other

Submissions summary: Benign:11 Other:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Glycogen storage disease, type II Benign:4 Other:3

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 23, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
other, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 02, 2019	- pseudodeficiency allele
not provided, no classification provided	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	Variant interpreted as Benign and reported on 08-27-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpreted as Benign, Pseudo-deficiency allele and reported, most recently on 12-16-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Jun 03, 2020	- -

not provided Benign:3 Other:2

Benign, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jun 02, 2017	The GAA gene is associated with Pompe disease; however, this variant is not associated with disease. It is known to interfere with assays for GAA enzyme activity and is therefore called a "pseudodeficiency allele". Even individuals with two copies of this variant do not have Pompe disease. -
other, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 14, 2017	- Variant classified as "other reportable" ??? variant is clinically benign (not associated with disease) but is reported when observed (e.g. pseudodeficiency alleles).
not provided, flagged submission	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	Variant reported in multiple Invitae PIN participants. Variant interpreted as Benign (Pseudo deficiency allele) most recently on 10/30/2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 04, 2018	Associated with pseudodeficiency of alpha-glucosidase enzyme. Homozygosity for D91N or compound heterozygosity for D91N and a pathogenic variant results in low enzyme activity but no clinical symptoms of Pompe disease (Martiniuk et al., 1990; Tajima et al., 2007; Kroos et al., 2008); This variant is associated with the following publications: (PMID: 31301153, 29181627, 25998610, 20080426, 2203258) -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Acid alpha-glucosidase, allele 2 Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Oct 28, 2012

- -

Cardiovascular phenotype Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 28, 2015

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Benign	-0.41	T
BayesDel_noAF	Benign	-0.34
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.51	D;.;D;D
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.87	D;D;.;D
MetaRNN	Benign	0.020	T;T;T;T
MetaSVM	Benign	-0.79	T
MutationAssessor	Benign	1.6	.;.;L;L
PrimateAI	Uncertain	0.67	T
PROVEAN	Uncertain	-4.3	.;.;D;D
REVEL	Uncertain	0.40
Sift	Benign	0.10	.;.;T;T
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	.;.;D;D
Vest4		0.40, 0.33
MPC		0.53
ClinPred		0.017	T
GERP RS		4.9
Varity_R		0.71
gMVP		0.83

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: rs1800299; hg19: chr17-78078656; COSMIC: COSV56408897; COSMIC: COSV56408897;