rs377544304

Positions:

• chr17-80112622-G-A
• chr17-80112622-G-C
• chr17-80112622-G-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1 PP4_Moderate PP3 PS3_Moderate PM2_Supporting PM3_Strong

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.1799G>A variant in GAA is a missense variant predicted to result in substitution of arginine by histidine at amino acid 600 (p.Arg600His).This variant has been reported in at least 7 patients including those with symptoms consistent with infantile onset Pompe disease, <10% GAA activity in muscle, and showing improvement on enzyme replacement therapy (PMID:15121988, 24715333); one patient identified on newborn screen with confirmatory GAA activity testing and showing cardiac hypertrophy and arrythmia on cardiac evaluation (PMID:33073007), three patients with features consistent with Pompe disease and GAA activity in the laboratory's affected range in dried blood spots or leukocytes (PMID:2267665, 33741225) (PP4_Moderate). Four patients are compound heterozygous for the variant and another variant in GAA, phase unknown, that has been classified a pathogenic by the ClinGen LSD VCEP including c.-32-13T>G (2 independent probands, PMIDs: 21967859, 2267665), c.2481+110_2646+39del) (2 independent probands, PMID:15121988, 24715333; PMID:2267665), and one homozygote (PMID:33073007) (PM3_Strong). In addition, two patients are compound heterozygous for the variant and another missense change, or c.1465G>A (p.Asp489Asn) (PMID:22711147) or c.1751A>C (p.His584Pro) (PMID:33741225). The allelic data from these patients will be used in the assessment of the other missense change and is not included here to avoid circular logic. The amino acid change was reported in additional patients but the cDNA changes were not provided and so the data is not included (PMID:10338092, 20033296).The highest population minor allele frequency in gnomAD is 0.00003 (1.30606 alleles) in the South Asian population, which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting).This variant alters the arginine at amino acid 600, a residue that crystallography studies have shown to be important important in the active site architecture and substrate binding of GAA, and therefore has been defined as a critical residue by the ClinGen LSD VCEP (https://www.biorxiv.org/content/10.1101/212837v1.full.pdf, PMID:29061980) (PM1).This variant results in <2% GAA activity when expressed in COS-7 and HEK 293 cells (PMID:19862843, 24715333), and was shown to be abnormally processed by Western blot analysis, with production of very little of the active 76 kDa form, when expressed in HEK293 cells (PMID:24715333). PS3_Moderate is applied based on two separate studies, one showing GAA deficiency and the other showing abnormal GAA processing (PS3_Moderate).The computational predictor REVEL gives a score of 0.967 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3).Three additional missense changes in the same codon have been reported in patients with Pompe disease. The classification of p.Arg600His will be used to to support the classification of the other variants c.1798C>T (p.Arg600Cys) (pathogenic based on classification by the ClinGen LSD VCEP), c.1799G>C (p.Arg600Pro) and c.1799G>T (p.Arg600Leu), and is not used here to avoid circular logic.There is a ClinVar entry for this variant (Variation ID: 370130) with 10 submitters classifying the variant as pathogenic and two as likely pathogenic.In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. GAA-specific ACMG-AMP crteria applied, as specified by the ClinGen LSD VCEP (Specification Version 2.0): PM3_Strong, PM1, PS3_Moderate, PP4_Moderate, PP3, PM2_Supporting.Classification approved by the ClinGen LSD VCEP on Oct 18, 2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA8815482/MONDO:0009290/010

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000096 (0 hom.)
• Consequence: GAA NM_000152.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:15
• Conservation: PhyloP100: 9.80

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 Pathogenic. Variant got 12 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM1: For more information check the summary or visit ClinGen Evidence Repository.
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAA	NM_000152.5	c.1799G>A	p.Arg600His	missense_variant	13/20	ENST00000302262.8	NP_000143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAA	ENST00000302262.8	c.1799G>A	p.Arg600His	missense_variant	13/20	1	NM_000152.5	ENSP00000305692	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000121 AC: 3 AN: 248322 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135152

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: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000179

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000958 AC: 14 AN: 1460678 Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6 AN XY: 726680

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000108

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000236 Hom.: 0

Bravo AF: 0.00000378

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:15

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 18, 2019	The GAA c.1799G>A; p.Arg600His variant (rs377544304) is reported in the literature in multiple individuals affected with glycogen storage disease type II, also known as Pompe disease, each of whom also carried a second pathogenic variant (de Vries 2011, Ko 1999, van der Beek 2008). This variant is reported as pathogenic/likely pathogenic by multiple laboratories in ClinVar (Variation ID: 370130), and it is found on only three chromosomes in the Genome Aggregation Database (3/248322 alleles), indicating it is not a common polymorphism. The arginine at codon 600 is highly conserved, and functional characterization of the variant protein expressed in cultured cells suggests it has less than 2% of wildtype activity (Flanagan 2009). Additionally, other amino acid substitutions at this codon (p.Arg600Cys, p.Arg600Leu) have been reported in individuals with Pompe disease and are considered disease-causing (Fukuhara 2017, McCready 2007). Based on available information, the p.Arg600His variant is considered to be pathogenic. References: de Vries JM et al. First experience with enzyme replacement therapy during pregnancy and lactation in Pompe disease. Mol Genet Metab. 2011 Dec;104(4):552-5. Flanagan JJ et al. The pharmacological chaperone 1-deoxynojirimycin increases the activity and lysosomal trafficking of multiple mutant forms of acid alpha-glucosidase. Hum Mutat. 2009 Dec;30(12):1683-92. Fukuhara Y et al. A molecular analysis of the GAA gene and clinical spectrum in 38 patients with Pompe disease in Japan. Mol Genet Metab Rep. 2017 Oct 31;14:3-9. Ko et al. Molecular genetic study of Pompe disease in Chinese patients in Taiwan. Hum Mutat. 1999;13(5):380-4. McCready ME et al. Development of a clinical assay for detection of GAA mutations and characterization of the GAA mutation spectrum in a Canadian cohort of individuals with glycogen storage disease, type II. Mol Genet Metab. 2007 Dec;92(4):325-35. van der Beek NA et al. Cardiac evaluation in children and adults with Pompe disease sharing the common c.-32-13T>G genotype rarely reveals abnormalities. J Neurol Sci. 2008 Dec 15;275(1-2):46-50. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 22, 2023	- -
Pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Arg600His variant in GAA has been reported in at least 12 individuals in the compound heterozygous state with Glycogen Storage Disease II (PMID: 22676651, 21920843, 18757064, 27649523, 24715333, 18995995, 10338092, 27649523, 15121988). This variant has also been reported pathogenic by GeneDx and Laboratorio de Medicina Genomica and likely pathogenic by Counsyl in ClinVar (Variation ID: 370130). This variant has been identified in 0.003% (1/30606) of South Asian chromosomes and 0.002% (2/111734) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs377544304). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies with COS and HEK cells transfected with this variant provide some evidence that the p.Arg600His variant may impact enzyme levels and activity (PMID: 19862843, 24715333). 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 presence of this variant in combination with pathogenic variants and in individuals with Glycogen Storage Disease II increases the likelihood that the p.Arg600His variant is pathogenic (PMID: 27649523, 22676651, 24715333). The phenotype of individuals heterozygous with this variant is highly specific for Glycogen Storage Disease II based on GAA activity assays (PMID: 24715333, 27649523, 15121988). One additional pathogenic variant, resulting in a different amino acid change at the same position, p.Arg600Cys, has been reported in association with disease in the literature, supporting that a change at this position may not be tolerated (PMID: 14643388, 24384324, 18458862, 14695532, 11053688, 21982629). In summary, this variant meets criteria to be classified as pathogenic for Glycogen Storage Disease II in an autosomal recessive manner based on in vitro functional studies and multiple occurrences with variants reported in association with disease in individuals with Glycogen Storage Disease II. ACMG/AMP Criteria applied: PS3, PM3, PM2, PP3, PP4 (Richards 2015). -
Likely pathogenic, no assertion criteria provided	clinical testing	Counsyl	Nov 24, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 29, 2020	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Oct 18, 2022	The NM_000152.5:c.1799G>A variant in GAA is a missense variant predicted to result in substitution of arginine by histidine at amino acid 600 (p.Arg600His). This variant has been reported in at least 7 patients including those with symptoms consistent with infantile onset Pompe disease, <10% GAA activity in muscle, and showing improvement on enzyme replacement therapy (PMID: 15121988, 24715333); one patient identified on newborn screen with confirmatory GAA activity testing and showing cardiac hypertrophy and arrythmia on cardiac evaluation (PMID: 33073007), three patients with features consistent with Pompe disease and GAA activity in the laboratory's affected range in dried blood spots or leukocytes (PMID: 2267665, 33741225) (PP4_Moderate). Four patients are compound heterozygous for the variant and another variant in GAA, phase unknown, that has been classified a pathogenic by the ClinGen LSD VCEP including c.-32-13T>G (2 independent probands, PMIDs: 21967859, 2267665), c.2481+110_2646+39del) (2 independent probands, PMID: 15121988, 24715333; PMID: 2267665), and one homozygote (PMID: 33073007) (PM3_Strong). In addition, two patients are compound heterozygous for the variant and another missense change, or c.1465G>A (p.Asp489Asn) (PMID: 22711147) or c.1751A>C (p.His584Pro) (PMID: 33741225). The allelic data from these patients will be used in the assessment of the other missense change and is not included here to avoid circular logic. The amino acid change was reported in additional patients but the cDNA changes were not provided and so the data is not included (PMID: 10338092, 20033296). The highest population minor allele frequency in gnomAD is 0.00003 (1.30606 alleles) in the South Asian population, which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting). This variant alters the arginine at amino acid 600, a residue that crystallography studies have shown to be important important in the active site architecture and substrate binding of GAA, and therefore has been defined as a critical residue by the ClinGen LSD VCEP (https://www.biorxiv.org/content/10.1101/212837v1.full.pdf, PMID: 29061980) (PM1). This variant results in <2% GAA activity when expressed in COS-7 and HEK 293 cells (PMID: 19862843, 24715333), and was shown to be abnormally processed by Western blot analysis, with production of very little of the active 76 kDa form, when expressed in HEK293 cells (PMID: 24715333). PS3_Moderate is applied based on two separate studies, one showing GAA deficiency and the other showing abnormal GAA processing (PS3_Moderate). The computational predictor REVEL gives a score of 0.967 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). Three additional missense changes in the same codon have been reported in patients with Pompe disease. The classification of p.Arg600His will be used to to support the classification of the other variants c.1798C>T (p.Arg600Cys) (pathogenic based on classification by the ClinGen LSD VCEP), c.1799G>C (p.Arg600Pro) and c.1799G>T (p.Arg600Leu), and is not used here to avoid circular logic. There is a ClinVar entry for this variant (Variation ID: 370130) with 10 submitters classifying the variant as pathogenic and two as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. GAA-specific ACMG-AMP crteria applied, as specified by the ClinGen LSD VCEP (Specification Version 2.0): PM3_Strong, PM1, PS3_Moderate, PP4_Moderate, PP3, PM2_Supporting. Classification approved by the ClinGen LSD VCEP on Oct 18, 2022). -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	Jun 22, 2023	The homozygous mis-sense variant c.1799 G>A (p.Arg600His) has been identified in a proband with cardiomegaly, respiratory distress, muscle weakness, difficulty in sitting from lying position, difficulty in standing from sitting position, proximal muscle weakness in upper and lower extremities, protuberant abdomen and hepatomegaly, . This variant has been found 0.0012%gnomAD (aggregated). This has been previously reported PMID: 31342611 -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 14, 2021	Variant summary: GAA c.1799G>A (p.Arg600His) results in a non-conservative amino acid change in 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 1.2e-05 in 248322 control chromosomes. c.1799G>A has been reported in the literature in multiple individuals affected with classic infantile, childhood, or adult forms of CRIM positive Glycogen Storage Disease, Type 2 (Pompe Disease) (example, Ko_1999, de Vries_2011, Monies_2019, Pompe disease variant database). These data indicate that the variant is very likely to be associated with disease. No experimental evidence demonstrating an impact on protein function was ascertained in the context of this evaluation. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=3)/likely pathogenic(n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Laboratorio de Medicina Genomica, Hospital General de Culiacan	-	The observed phenotype is merely musculoskeletal. Dyspnea on exertion, difficulty in both genuflection and climbing stairs, progressive muscle weakness in pelvic area, amyotrophy, hyperflexia, early fatigue, myalgias and cramps, Gowers sign were observed in all siblings, while weakness in arms, scapula alata and progresive muscle weakness in scapula area were observed in males only. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 04, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 600 of the GAA protein (p.Arg600His). This variant is present in population databases (rs377544304, gnomAD 0.003%). This missense change has been observed in individual(s) with Pompe disease (PMID: 10338092, 20033296, 30155607, 31342611). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 370130). 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 have shown that this missense change affects GAA function (PMID: 19862843). This variant disrupts the p.Arg600 amino acid residue in GAA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10338092, 21039225, 21232767, 21439876). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:5

Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Dec 15, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 10, 2017	The R600H pathogenic variant in the GAA gene has been previously reported in multiple unrelated individuals with GSDII, who harbored a pathogenic variant on the opposite GAA allele (Ko et al., 1999; van der Beek et al., 2008). Analysis of R600H transfected COS-7 cells demonstrates less than 2% residual GAA enzyme activity compared to wildtype controls (Flanagan et al., 2009). The R600H variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species and different missense variants at the same position (R600C/L) have been previously reported in the homozygous and compound heterozygous state in individuals with GSDII (Tsujino et al., 2000; McCready et al., 2007). Additionally, the majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014). In silico analysis predicts this variant is probably damaging to the protein structure/function. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 21, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.81
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.98	D;D
Eigen	Pathogenic	0.99
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	.;D
M_CAP	Pathogenic	0.69	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	5.2	H;H
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.69	T
PROVEAN	Pathogenic	-4.9	D;D
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.0020	D;D
Polyphen		1.0	D;D
Vest4		0.99
MVP		1.0
MPC		0.60
ClinPred		1.0	D
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.97
gMVP		0.95

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: rs377544304; hg19: chr17-78086421; COSMIC: COSV56406566; COSMIC: COSV56406566;