rs368438393

chr17-80112920-G-Achr17-80112920-G-Cchr17-80112920-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000152.5(GAA):c.1933G>A(p.Asp645Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,610,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D645E) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: GAA NM_000152.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:12
• Conservation: PhyloP100: 9.82

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 18 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000152.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-80112922-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 4029.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.978
• PP5: Variant 17-80112920-G-A is Pathogenic according to our data. Variant chr17-80112920-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 188728.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-80112920-G-A is described in Lovd as [Pathogenic]. Variant chr17-80112920-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAA	NM_000152.5	c.1933G>A	p.Asp645Asn	missense_variant	14/20	ENST00000302262.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8	c.1933G>A	p.Asp645Asn	missense_variant	14/20	1	NM_000152.5	P1

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152196 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000483

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: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000825 AC: 2 AN: 242414 Hom.: 0 AF XY: 0.0000152 AC XY: 2 AN XY: 131818

Gnomad AFR exome AF: 0.0000660

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000915

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000123 AC: 18 AN: 1458274 Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10 AN XY: 725104

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: 0.0000351

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000117

Gnomad4 OTH exome AF: 0.0000332

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152196 Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1 AN XY: 74352

Gnomad4 AFR AF: 0.0000483

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: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000272 Hom.: 0

Bravo AF: 0.0000302

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.0000247 AC: 3

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: reviewed by expert panel

Submissions by phenotype

Glycogen storage disease, type II Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 10, 2018	Variant summary: GAA c.1933G>A (p.Asp645Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.3e-05 in 86510 control chromosomes (ExAC). c.1933G>A has been reported in the literature in compound heterozygous or homozygous state in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (e.g. Huie 1998, Prater 2012, McCready 2007). These data indicate that the variant is very likely to be associated with disease. Several publications also reported experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (e.g. Huie 1998, Prater 2012, McCready 2007). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and both laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 17, 2023	- -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Mar 21, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 09, 2022	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	May 28, 2020	This variant, c.1933G>A (p.Asp645Asn), is a missense change which has been reported in least 11 individuals with deficient GAA activity meeting the ClinGen LSD VCEP's specifications for PP4 (PMIDs 9535769, 15145338, 16860134, 17723315, 23601496, 25139343, 26497565). Five of these individuals are homozygous for the variant have been reported to have infantile onset Pompe disease (PMIDs 16860134, 25139343, 26497565). This variant was also found in two patients who meet PP4 specifications, in compound heterozygosity, phase not confirmed, with a unique pathogenic variant in GAA, either c.2501_2502del or c.2242dup (PMIDs 9535769, 23601496). Based on data from homozygous and compound heterozygous patients, PM3_Strong is met. Additional compound heterozygous cases have been reported but the in trans data has been used in the assessment of the second variant and therefore is not included here in order to avoid circular logic (PMIDs 15145338, 17723315, 26497565). Other cases were not included because the residual GAA activity was not provided, and therefore PP4 cannot be assessed (PMIDs 18429042, 25455803, 27927596, 29122469, 30105547, 30155607). The highest population minor allele frequency in gnomAD is 0.00007 in the African population, meeting PM2. When expressed in GAA-deficient fibroblasts and COS cells, this variant results in virtually no GAA activity (PMIDs 9535769, 15145338), meeting PS3. The score for the in silico meta-predictor, REVEL, is 0.868 suggesting that the variant impacts the function of GAA, meeting PP3. Three other amino acid changes have been reported in patients with Pompe disease at the same amino acid position (c.1933G>C (p.Asp645His), c.1933G>T (p.Asp645Tyr), c.1935C>A (p.Asp645Glu). At least one of these variants, c.1935C>A (p.Asp645Glu), is pathogenic, meeting PM5. In summary, this variant meets the criteria to be specified as pathogenic for Pompe disease. ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PS3, PM2, PM3_Strong, PM5, PP4. -
Pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Asp645Asn variant in GAA has been reported in at least 29 individuals with Glycogen Storage Disease II (PMID: 9535769, 10338092, 15145338, 16860134, 18429042, 17723315, 20830524, 26497565, 23601496, 25139343, 30155607, 19862843, 27927596, 25455803, 30105547, 29122469). This variant has been identified in 0.007% (1/15154) of African chromosomes and 0.001% (1/109242) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs368438393). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. The presence of this variant in homozygotes and in combination with reported pathogenic variants and in individuals with Glycogen Storage Disease II increases the likelihood that the p.Asp645Asn variant is pathogenic (PMID: 20830524, 17723315, 16860134, 15145338, 26497565, 25139343, 9535769, 23601496). This variant has also been reported likely pathogenic by Counsyl and pathogenic by GeneDx, Illumina, Invitae, and Integrated Genetics in ClinVar (Variation ID: 188728). In vitro functional studies with COS cells transfected with this variant provide some evidence that the p.Asp645Asn variant may impact protein function based on GAA activity assays and a Western Blot (PMID: 15145338, 9535769). 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 phenotype of individuals with Glycogen Storage Disease II and homozygous or heterozygous for this variant based on very low GAA activity, consistent with disease (PMID: 20830524, 17723315, 16860134, 15145338, 26497565, 25139343, 9535769, 23601496). Three additional variants at the the same position (p.Asp645Glu, p.Asp645Tyr, and p.Asp645His) have been reported in association with disease in ClinVar, supporting that a change at this position may not be tolerated (Variation ID: 4029, 189013, 556386). In summary, this variant meets criteria to be classified as pathogenic for Glycogen Storage Disease II in an autosomal recessive manner based on multiple occurrences with reported pathogenic or likely pathogenic variants in individuals with Glycogen Storage Disease II, in vitro functional studies, and multiple missense variants associated with disease at the same position. ACMG/AMP Criteria applied: PM3_Strong, PM5_Strong, PS3, PM2, PP3, PP4 (Richards 2015). -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	May 10, 2017	The GAA c.1933G>A (p.Asp645Asn) variant has been reported in six studies and is found in a total of seven patients with infantile-onset Pompe disease (also known as glycogen storage disease, type II). The p.Asp645Asn variant was present in five patients in a compound heterozygous state and two patients in a homozygous state (Huie et al. 1998; Kroos et al. 2004; McCready et al. 2007; Pittis et al. 2008; Del Rizzo et al. 2010; Tan et al. 2015). In addition, two unaffected parents carried the variant in a heterozygous state (Kroos et al. 2004; Tan et al. 2015). Control data are unavailable for the p.Asp645Asn variant, which is reported at a frequency of 0.00023 in the African population of the Exome Sequencing Project, but this is based on one allele in a region of low sequence coverage. In vitro expression of the p.Asp645Asn variant in both SV40 immortalized fibroblasts (TR4912) and COS cells yielded low enzyme activity (Huie et al. 1998; Kroos et al. 2004). Based on the collective evidence, the p.Asp645Asn variant is classified as pathogenic for glycogen storage disease, type II. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 03, 2023	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 645 of the GAA protein (p.Asp645Asn). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individuals with Pompe disease (PMID: 9535769, 15145338, 17723315, 18429042, 20830524, 23787031). ClinVar contains an entry for this variant (Variation ID: 188728). 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. Experimental studies have shown that this missense change affects GAA function (PMID: 9535769, 15145338, 17723315, 20830524). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	Mar 18, 2023	A homozygous missense variant in exon 14 of the GAA gene that results in the amino acid substitution of Asparagine for Aspartate at codon 645 was detected. The observed variant c.1933G>A (p.Asp645Asn) has not been reported in the 1000 genomes and has a MAF of 0.0008% in the gnomAD databases. The in-silico prediction of the variant are damaging by PolyPhen-2 (HumDiv) and damaging by SIFT, LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 07, 2017	The D645N pathogenic variant in the GAA gene has been previously reported, in both the compound heterozygous and homozygous state, in patients with infantile GSDII (Huie et al., 1998; Del Rizzo et al., 2010). Functional studies demonstrate D645N results in significantly reduced GAA enzyme activity compared to wild type controls (Huie et al., 1998). The D645N 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 semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and different missense variants at the same position (D645H/Y/E) have been previously reported in association with GSDII (Lin et al., 1995; Gort et al., 2007; Hermans et al., 1993). Additionally, in silico analysis predicts this variant is probably damaging to the protein structure/function. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 07, 2023	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.72
BayesDel_addAF	Pathogenic	0.16	D
BayesDel_noAF	Pathogenic	0.18
Cadd	Pathogenic	32
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.97	D;D
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Pathogenic	0.58	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	H;H
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.75	T
PROVEAN	Pathogenic	-4.9	D;D
REVEL	Pathogenic	0.87
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.99
MVP		1.0
MPC		0.54
ClinPred		0.99	D
GERP RS		4.7
Varity_R		0.95
gMVP		0.96

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: rs368438393; hg19: chr17-78086719;