rs786204720

Positions:

• chr17-80110945-T-C

Variant summary

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

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.1556T>C variant in GAA is a missense variant predicted to cause substitution of methionine by threonine at amino acid 519 (p.Met519Thr). This variant has been detected in at least 4 individuals with Pompe disease. Of those individuals, 3 were compound heterozygous for the variant and a variant that has been classified as pathogenic by the ClinGen LD VCEP, phase unconfirmed, either c.525del (ClinVar Variation ID: 4033, SCV001443331.1) (PMID:14695532), c.1441T>C (p.Trp481Arg) (ClinVar Variation ID: 189007, SCV004227917.1) (PMID:31086307), or c.[752C>T;761C>T] (p.[Ser251Leu;Ser254Leu] (ClinVar Variation ID 325781/325782) (Clinical laboratory data); One individual was homozygous for the variant (PMID:33741225) (PM3_Strong). At least 1 patient with this variant had documented GAA deficiency with <10% of normal mean control level of GAA activity in dried blood spot (PMID:33741225) and 2 patients were reported to have symptoms consistent with infantile onset Pompe disease (PMID:14695532) (PP4_Moderate). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/30616 alleles) in the South Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.983 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). Expression of the variant in COS-7 resulted in <2% wild type GAA activity with western blot data showing decreased level of mature protein, indicating that this variant may impact protein function (PMIDs: 19862843, 14695532) (PS3_Moderate). This variant alters amino acid M519, a residue that crystallography studies have shown to be important in the active site of GAA, and therefore has been defined as a critical residue by the ClinGen Lysosomal Diseases VCEP (https://www.biorxiv.org/content/10.1101/212837v1.full.pdf, PMID:29061980) (PM1). There is a ClinVar entry for this variant (Variation ID: 189124). In summary, this variant meets the criteria to be classified as Pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria met, based on the specification of the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): PM3_strong, PP4_moderate, PM1, PS3_moderate, PP3, PM2_supporting.(Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on May 7, 2024) LINK:https://erepo.genome.network/evrepo/ui/classification/CA274402/MONDO:0009290/010

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: GAA NM_000152.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:11 U:1
• Conservation: PhyloP100: 6.02

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.1556T>C	p.Met519Thr	missense_variant	11/20	ENST00000302262.8	NP_000143.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAA	ENST00000302262.8	c.1556T>C	p.Met519Thr	missense_variant	11/20	1	NM_000152.5	ENSP00000305692.3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152156 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000796 AC: 2 AN: 251282 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135862

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: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461648 Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2 AN XY: 727110

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152156 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74334

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:9

Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Jan 14, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). The variant is in trans with NM_000152.5:c.1561G>A variant. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.98; 3Cnet: 0.92). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000189124). Different missense changes at the same codon (p.Met519Ile, p.Met519Val) have been reported to be associated with GAA related disorder (ClinVar ID: VCV001067893 / PMID: 31965297, 7866409). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	Oct 15, 2020	Met519Thr has been reported by Reuser et. al. 1995 PMID:7603530 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 29, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 04, 2023	Experimental studies have shown that this missense change affects GAA function (PMID: 14695532, 19862843). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Met519 amino acid residue in GAA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 31439017, 31965297; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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. ClinVar contains an entry for this variant (Variation ID: 189124). This missense change has been observed in individual(s) with Pompe disease (PMID: 31086307, 33741225). This variant is present in population databases (rs786204720, gnomAD 0.003%). This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 519 of the GAA protein (p.Met519Thr). -
Likely pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 29, 2020	The p.Met519Thr variant in GAA has been reported in 3 individuals (1 Australian, 1 Dutch, and 1 Belgian) with Glycogen Storage Disease II (PMID: 14695532), and has been identified in 0.003% (1/30616) of South Asian chromosomes and 0.001% (1/113600) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs786204720). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported likely pathogenic by Counsyl and a VUS by EGL in ClinVar (Variation ID: 189124). This variant is located in the highly conserved GH31 motif, a region involved in substrate binding (PMID: 19862843, 15501829). In vitro functional studies provide some evidence that the p.Met519Thr variant may impact protein function (PMID: 19862843, 14695532). 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. One additional variant at the the same position, p.Met519Val, has been reported in association with disease in the literature, slightly supporting that a change at this position may not be tolerated (PMID: 19862843, 14695532). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PS3, PM2, PP3, PM5_Supporting (Richards 2015). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	May 07, 2024	The NM_000152.5:c.1556T>C variant in GAA is a missense variant predicted to cause substitution of methionine by threonine at amino acid 519 (p.Met519Thr). This variant has been detected in at least 4 individuals with Pompe disease. Of those individuals, 3 were compound heterozygous for the variant and a variant that has been classified as pathogenic by the ClinGen LD VCEP, phase unconfirmed, either c.525del (ClinVar Variation ID: 4033, SCV001443331.1) (PMID: 14695532), c.1441T>C (p.Trp481Arg) (ClinVar Variation ID: 189007, SCV004227917.1) (PMID: 31086307), or c.[752C>T;761C>T] (p.[Ser251Leu;Ser254Leu] (ClinVar Variation ID 325781/325782) (Clinical laboratory data); One individual was homozygous for the variant (PMID: 33741225) (PM3_Strong). At least 1 patient with this variant had documented GAA deficiency with <10% of normal mean control level of GAA activity in dried blood spot (PMID: 33741225) and 2 patients were reported to have symptoms consistent with infantile onset Pompe disease (PMID: 14695532) (PP4_Moderate). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/30616 alleles) in the South Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.983 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). Expression of the variant in COS-7 resulted in <2% wild type GAA activity with western blot data showing decreased level of mature protein, indicating that this variant may impact protein function (PMIDs: 19862843, 14695532) (PS3_Moderate). This variant alters amino acid M519, a residue that crystallography studies have shown to be important in the active site of GAA, and therefore has been defined as a critical residue by the ClinGen Lysosomal Diseases VCEP (https://www.biorxiv.org/content/10.1101/212837v1.full.pdf, PMID: 29061980) (PM1). There is a ClinVar entry for this variant (Variation ID: 189124). In summary, this variant meets the criteria to be classified as Pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria met, based on the specification of the ClinGen Lysosomal Diseases VCEP (Specifications Version 2.0): PM3_strong, PP4_moderate, PM1, PS3_moderate, PP3, PM2_supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on May 7, 2024) -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Feb 14, 2023	The missense variant c.1556T>C(p.Met519Thr) in GAA gene has been reported in homozygous state in individuals with Pompe disease (Puri RD, et al., 2021).Experimental studies have shown that this missense change affects GAA function. This variant disrupts the p.Met519 amino acid residue in GAA (Flanagan JJ,et al., 2009). The variant has 0.001% allele frequency in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Uncertain significance/ Likely Pathogenic/ Pathogenic.The amino acid Methionine at position 519 is changed to a Threonine changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by SIFT. The amino acid change p.Met519Thr in GAA is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:2 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 08, 2024	Published functional studies demonstrate that the variant results in significantly reduced enzyme activity (PMID: 19862843); Not observed at significant frequency in large population cohorts (gnomAD); 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: 7603530, 14695532, 31086307, 31439017, 31193175, 15501829, 31254424, 33741225, 31965297, 19862843, 19343043, 22253258) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 28, 2023	- -
Uncertain significance, flagged submission	clinical testing	Eurofins Ntd Llc (ga)	Nov 02, 2016	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.48
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.98	D;D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.89
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	.;D
M_CAP	Pathogenic	0.79	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.5	H;H
PrimateAI	Pathogenic	0.80	T
PROVEAN	Pathogenic	-6.0	D;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.98
MutPred		0.94		Gain of glycosylation at M519 (P = 0.025);Gain of glycosylation at M519 (P = 0.025);
MVP		1.0
MPC		0.58
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.98
gMVP		0.98

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: rs786204720; hg19: chr17-78084744;