rs543360994

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2_SupportingPM3_SupportingPP4_Moderate

This summary comes from the ClinGen Evidence Repository: The NM_000152.5:c.781G>A variant in GAA is a missense variant predicted to cause substitution of Ala by Thr at amino acid 261 (p.Ala261Thr). One patient with infantile-onset Pompe disease who was homozygous for this variant has been reported;, the parents were confirmed to be heterozygous (PMID 31510962) (PM3_Supporting). The patients symptoms included dyspnea, poor feeding, failure to thrive, delayed motor milestone, short PR interval, biventricular hypertrophy, and severe intellectual disability. GAA activity was 0.43% of normal (PMID 31510962)(PP4_Moderate). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00010 (3/30616 alleles) in the South Asian population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). When expressed in COS cells, the variant results in reduced GAA activity (66% in cell extract and 5% in culture medium comparing to wildtype) and is classified as class D for the severity rating (PMID 31510962) (BS3_Supporting). The computational predictor REVEL gives a score of 0.584 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function. The computational splicing predictor SpliceAI predicts no impact on splicing. Two different missense variants, c.781G>C (p.Ala261Pro) and c.782C>T (p.Ala261Val) in the same codon have been reported in patients with Pompe disease. However, these variants have not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen LSD VCEP (PM5 not met). There is a ClinVar entry for this variant (Variation ID: 456438). In summary, this variant meets the criteria to be classified as Uncertain significance for Pompe disease based on the ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Storage Disorders Variant Curation Expert panel (Specification Version 2.0): PM2_supporting, PM3_supporting, PP4_Moderate, BS3_supporting.(Classification approved by the ClinGen LSD VCEP on Nov 1, 2022). LINK:https://erepo.genome.network/evrepo/ui/classification/CA8815016/MONDO:0009290/010

Frequency

Genomes: 𝑓 0.000039 ( 0 hom., cov: 34)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

GAA
NM_000152.5 missense

Scores

Clinical Significance

Uncertain significance reviewed by expert panel P:2U:4

Conservation

PhyloP100: 9.85

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

PM3

PP4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAA	NM_000152.5 linkuse as main transcript	c.781G>A	p.Ala261Thr	missense_variant	4/20	ENST00000302262.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAA	ENST00000302262.8 linkuse as main transcript	c.781G>A	p.Ala261Thr	missense_variant	4/20	1	NM_000152.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0000394

AC:

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000199

AC:

AN:

251028

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135848

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0000980

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000882

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000110

AC:

AN:

1460800

Hom.:

Cov.:

AF XY:

0.0000151

AC XY:

AN XY:

726732

show subpopulations

Gnomad4 AFR exome

AF:

0.0000598

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0000348

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000809

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000394

AC:

AN:

152286

Hom.:

Cov.:

AF XY:

0.0000537

AC XY:

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0000722

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000986

Hom.:

Bravo

AF:

0.0000378

ExAC

AF:

0.0000247

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:2Uncertain:4

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Glycogen storage disease, type II

Pathogenic:2Uncertain:2

Pathogenic, no assertion criteria provided	in vitro;research	Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine Ramathibodi Hospital, Mahidol University	Jul 10, 2019	The c.781G>A (p.A261T) is present in population database (rs543360994, ExAC 0.00002%). This variant has not been reported in the literature in individuals with GAA-related disease. ClinVar contains an entry for this variant (Variation ID: 456438). It was reported to have uncertain impact on protein function and there is no indication that it causes disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, Polyphen-2, PredictSNP2, CADD, DANN, FATHMM, and FunSeq2) all suggest that this variant is damaging/deleterious. Our study provided evident supported the impact of amino acid substitution at this position on GAA function. In vitro expression analysis of c.781G>A (p.A261T) indicates that this variant yielded partial reduction of enzyme activity and impaired GAA processing and transportation. We interpret c.781G>A (p.A261T) as a pathogenic variant. -
Uncertain significance, reviewed by expert panel	curation	ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	Nov 01, 2022	The NM_000152.5:c.781G>A variant in GAA is a missense variant predicted to cause substitution of Ala by Thr at amino acid 261 (p.Ala261Thr). One patient with infantile-onset Pompe disease who was homozygous for this variant has been reported;, the parents were confirmed to be heterozygous (PMID 31510962) (PM3_Supporting). The patients symptoms included dyspnea, poor feeding, failure to thrive, delayed motor milestone, short PR interval, biventricular hypertrophy, and severe intellectual disability. GAA activity was 0.43% of normal (PMID 31510962)(PP4_Moderate). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00010 (3/30616 alleles) in the South Asian population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). When expressed in COS cells, the variant results in reduced GAA activity (66% in cell extract and 5% in culture medium comparing to wildtype) and is classified as class D for the severity rating (PMID 31510962) (BS3_Supporting). The computational predictor REVEL gives a score of 0.584 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function. The computational splicing predictor SpliceAI predicts no impact on splicing. Two different missense variants, c.781G>C (p.Ala261Pro) and c.782C>T (p.Ala261Val) in the same codon have been reported in patients with Pompe disease. However, these variants have not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen LSD VCEP (PM5 not met). There is a ClinVar entry for this variant (Variation ID: 456438). In summary, this variant meets the criteria to be classified as Uncertain significance for Pompe disease based on the ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Storage Disorders Variant Curation Expert panel (Specification Version 2.0): PM2_supporting, PM3_supporting, PP4_Moderate, BS3_supporting. (Classification approved by the ClinGen LSD VCEP on Nov 1, 2022). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 16, 2023	This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 261 of the GAA protein (p.Ala261Thr). This variant is present in population databases (rs543360994, gnomAD 0.01%). This missense change has been observed in individual(s) with Pompe disease (PMID: 31510962). ClinVar contains an entry for this variant (Variation ID: 456438). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GAA protein function. Experimental studies have shown that this missense change affects GAA function (PMID: 31510962). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Nov 24, 2021	- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

May 19, 2023

Variant summary: GAA c.781G>A (p.Ala261Thr) results in a non-conservative amino acid change located in the Glycoside hydrolase family 31, N-terminal domain (IPR025887) of 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 2e-05 in 251028 control chromosomes (gnomAD). c.781G>A has been reported in the literature in a homozygous individual affected with infantile Glycogen Storage Disease (Pompe Disease) (example: Ngiwsara_2019). These data indicate that the variant may be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 31510962, 16865695). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=3) and pathogenic/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Nov 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.013

BayesDel_noAF

Uncertain

-0.050

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.15

T;D;D

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.38

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.90

D;.;D

M_CAP

Pathogenic

0.32

MetaRNN

Uncertain

0.60

D;D;D

MetaSVM

Uncertain

0.48

MutationAssessor

Uncertain

2.6

.;M;M

MutationTaster

Benign

0.84

D;D

PrimateAI

Benign

0.41

PROVEAN

Benign

-2.2

.;N;N

REVEL

Uncertain

0.58

Sift

Uncertain

0.0030

.;D;D

Sift4G

Uncertain

0.021

D;D;D

Polyphen

0.90

.;P;P

Vest4

0.61

MVP

0.98

MPC

0.35

ClinPred

0.76

GERP RS

5.1

Varity_R

0.67

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

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