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Variant: NM_000152.5(GAA):c.710C>T (p.Ala237Val)

CA116619

4035 (ClinVar)

Gene: GAA
Condition: glycogen storage disease II
Inheritance Mode: Autosomal recessive inheritance
UUID: 9ded6270-3579-4f65-8f8f-1f00020a7b23
Approved on: 2022-11-02
Published on: 2022-12-20

HGVS expressions

NM_000152.5:c.710C>T
NM_000152.5(GAA):c.710C>T
NM_000152.5(GAA):c.710C>T (p.Ala237Val)
NC_000017.11:g.80107574C>T
CM000679.2:g.80107574C>T
NC_000017.10:g.78081373C>T
CM000679.1:g.78081373C>T
NC_000017.9:g.75695968C>T
NG_009822.1:g.11019C>T
ENST00000302262.8:c.710C>T
ENST00000302262.7:c.710C>T
ENST00000390015.7:c.710C>T
ENST00000570803.5:c.710C>T
NM_000152.3:c.710C>T
NM_001079803.1:c.710C>T
NM_001079804.1:c.710C>T
NM_000152.4:c.710C>T
NM_001079803.2:c.710C>T
NM_001079804.2:c.710C>T
NM_001079803.3:c.710C>T
NM_001079804.3:c.710C>T

Uncertain Significance

Met criteria codes 3
PP4_Moderate PM3_Supporting PM2_Supporting
Not Met criteria codes 3
BP4 PS3 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000152.5:c.710C>T variant in GAA is a missense variant that is predicted to result in the substitution of alanine by valine at amino acid 237 (p.Ala237Val). A patient with late onset Pompe disease and this variant has been described with a severely reduced GAA activity (<10% normal) and an increase of total glycogen in muscle (PMID: 15668445, 17573812, 17643989) (PP4_Moderate). This patient is compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen LSD VCEP, c.877G>A (p.Gly293Arg) (PMID: 15668445, 17573812, 17643989) (PM3_Supporting). Another patient has been reported who is compound heterozygous for the variant and p.Met173del (PMID: 28196920). However, the cDNA changes for these variants were not provided and therefore the data was not included. The highest population minor allele frequency in gnomAD v2.1.1. is 0.00013 (4/30616 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). When expressed in COS cells, this variant had "greater than 2% wild-type GAA activity", but the activity was not provided (PS3 not met). The computational predictor REVEL gives a score of 0.693 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function (neither PP3 nor BP4 is met). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease. GAA-specific ACMG-AMP criteria met, as specified by the ClinGen LSD VCEP (Specifications Version 2.0): PP4_Moderate, PM2_Supporting, PM3_Supporting. (Classification approved by the ClinGen LSD VCEP on November 2, 2022)
Met criteria codes
PP4_Moderate
A patient with late onset Pompe diseaes and this variant has been described with a severely reduced GAA activity in muscle (<10% activity) and an increase of total glycogen (PMID: 15668445, 17573812, 17643989) (PP4_Moderate)
PM3_Supporting
A patient with late onset Pompe disease has been reported who is compound heterozygous for the variant and another variant in GAA that has been classified as pathogenic by the ClinGen LSD VCEP, c.877G>A (p.Gly293Arg) (PMID: 15668445, 17573812, 17643989). The phase is unknown. 0.5 points for PM3 (PM3_Supporting). Another patient has been reported who is compound heterozygous for the variant and p.Met173del (PMID: 28196920). However, the cDNA changes for these variants were not provided and therefore the data was not included.
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1. is 0.00013 (4/30616 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).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.693 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function.
PS3
When expressed in COS cells, this variant had "greater than 2% wild-type GAA activity", and was not responsive to the chaperone DNJ. Because further details on the residual GAA activity for this variant are not available, PS3 cannot be fully evaluated and therefore the criterion is not met at the current time.
PP3
The computational predictor REVEL gives a score of 0.693 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function.
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