17-80105089-G-A

Position:

chr17-80105089-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PM5BP4_Moderate

The NM_000152.5(GAA):c.503G>A(p.Arg168Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,611,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R168L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

GAA
NM_000152.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:8

Conservation

PhyloP100: -0.264

Variant links:

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]

GAA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr17-80105089-G-C is described in Lovd as [Likely_pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.097560704).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAA	NM_000152.5 linkuse as main transcript	c.503G>A	p.Arg168Gln	missense_variant	2/20	ENST00000302262.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8 linkuse as main transcript	c.503G>A	p.Arg168Gln	missense_variant	2/20	1	NM_000152.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

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:

0.000127

AC:

AN:

243198

Hom.:

AF XY:

0.000143

AC XY:

AN XY:

133026

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000290

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00153

Gnomad SAS exome

AF:

0.0000328

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000166

GnomAD4 exome

AF:

0.0000308

AC:

AN:

1459700

Hom.:

Cov.:

AF XY:

0.0000344

AC XY:

AN XY:

726158

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000781

Gnomad4 SAS exome

AF:

0.0000696

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000360

Gnomad4 OTH exome

AF:

0.0000331

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152204

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000192

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000793

ExAC

AF:

0.000141

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:8

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Glycogen storage disease, type II

Pathogenic:1Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The GAA c.503G>A (p.Arg168Gln) variant has been reported in two studies. Liu et al. (2013) identified the p.Arg168Gln variant in a compound heterozygous state with a second missense variant in one individual and in a heterozygous state in a second individual, both with glycogen storage disease type II. These individuals also carried a stop-gained variant whose zygosity and phase were not reported. In a subsequent study, Liu et al. (2014) reported the variant in a compound heterozygous state with a different second missense variant in two additional unrelated affected individuals. The p.Arg168Gln variant was found in a heterozygous state in two of 100 controls (Liu et al. 2013), and is reported at a frequency of 0.00178 in the East Asian population of the Exome Aggregation Consortium. The evidence for this variant is limited. The p.Arg168Gln variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for glycogen storage disease type II. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Jan 25, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 06, 2020	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The heterozygous p.Arg168Gln variant in GAA has been reported in at least 3 Chinese individuals with Glycogen Storage Disease II (PMID: 25526786, 24169249). This variant has been reported as a VUS by Invitae and Illumina in ClinVar (Variation ID: 325778), and has been identified in 0.146% (29/19820) of East Asian chromosomes, 0.003% (1/30464) of South Asian chromosomes, and 0.003% (1/35330) of Latino chromosomes chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs376685205). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools, including splice predictors, and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. The Arginine (Arg) at position 168 is not highly conserved in mammals and evolutionary distant species, and 19 species (including prairie vole, golden hamster, mouse, rat, panda, shrew, and zebrafish) carry a Glutamine (Gln), raising the possibility that this change at this position may be tolerated. Another VUS, p.Arg168Pro, at this position has been reported in association with Glycogen Storage Disease II in ClinVar and the literature (Variation ID: 639915; PMID: 25526786). This variant was reported in combination with a pathogenic variant and in 2 individuals with Glycogen Storage Disease II (PMID: 25526786). In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: BP4 (Richards 2015). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 28, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 168 of the GAA protein (p.Arg168Gln). This variant is present in population databases (rs376685205, gnomAD 0.1%). This missense change has been observed in individuals with glycogen storage disease type II (PMID: 21488292, 24169249, 25526786, 31076647; Invitae). ClinVar contains an entry for this variant (Variation ID: 325778). 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 not expected to disrupt GAA protein function with a negative predictive value of 95%. Studies have shown that this missense change does not affect mRNA splicing (PMID: 31301153). This variant disrupts the p.Arg168 amino acid residue in GAA. Other variant(s) that disrupt this residue have been observed in individuals with GAA-related conditions (PMID: 25526786, 30155607), which suggests that this may be a clinically significant amino acid residue. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

not provided

Uncertain:2

Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Aug 02, 2017	Testing for our patient was performed at Invitae. it has been seen in our center in one patient with HCM. Given the weak case data, its frequency in population databases, and presence of only one variant in a gene that followed autosomal recessive inheritance, we consider this variant a variant of uncertain significance, probably benign and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The GAA gene is associated with autosomal recessive Pompe disease. The variant has been seen in at least 1 unrelated cases of Pompe disease, and 1 case with reported reduced alpha-glucosidase activity. It has not been reported in any patient with HCM (not including this patient's family). There is weak case data and no segregation data. Niu et al. (2010), which is essentially a list of reported variants includes this variant with the comment: "The patientâ€™s mononuclear blood cell acid alpha-glucosidase activity was very low and found this mutation in GAA gene." No additional clinical information is provided. Author group is from Taiwan. Liu et al. (2013) reports this variant in a Chinese patient diagnosed with Pompe disease. The variant was also reported in 2/100 normal controls included in the study. The full text of the paper was only available in Chinese, but that info could be gathered from the abstract in English. Per the lab report: "Algorithms developed to predict the effect of missense changes on protein structure and function output thefollowing: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. The variant is present in 30 of 134,586 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Latino, and Ashkenazi descent. Specifically the variant has been seen in 27 of 9375 East Asian individuals (MAF = 0.144%) The average coverage at that site in gnomAD is 75x for exomes and 33x for genomes. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 03, 2023	In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21488292, 24169249, 31301153, 25526786) -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Nov 25, 2022

Variant summary: GAA c.503G>A (p.Arg168Gln) results in a conservative amino acid change located in the galactose mutarotase, N-terminal barrel domain (IPR031727) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00013 in 243198 control chromosomes, predominantly at a frequency of 0.0015 within the East Asian subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (0.00013 vs 0.0042), allowing no conclusion about variant significance. c.503G>A has been reported in the literature in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease), and in at least two cases it was found together with a pathogenic variant, however it was not reported whether phase was determined (e.g. Liu_2013, Liu_2014). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. The majority classified the variant as VUS, and one classified it as likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Benign

-0.13

CADD

Benign

0.94

DANN

Uncertain

0.99

DEOGEN2

Benign

0.19

T;.;T;T

Eigen

Benign

-0.94

Eigen_PC

Benign

-0.91

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.74

T;T;.;T

M_CAP

Benign

0.039

MetaRNN

Benign

0.098

T;T;T;T

MetaSVM

Benign

-0.86

MutationAssessor

Benign

0.88

.;.;L;L

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.18

PROVEAN

Benign

-0.020

.;.;N;N

REVEL

Uncertain

0.50

Sift

Benign

0.55

.;.;T;T

Sift4G

Benign

0.64

T;T;T;T

Polyphen

0.0070

.;.;B;B

Vest4

0.10, 0.10

MutPred

0.81

Loss of disorder (P = 0.1965);Loss of disorder (P = 0.1965);Loss of disorder (P = 0.1965);Loss of disorder (P = 0.1965);

MVP

0.81

MPC

0.13

ClinPred

0.031

GERP RS

-0.81

Varity_R

0.060

gMVP

0.37

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over