Variants

Pompe disease GAA variant database

Variants

Link to Pubmed

Location

exon 9

DNA nomenclature

c.1437G>A

RNA nomenclature

r.[1437g>a, 1327_1437del]

Protein nomenclature

p.[(=), (Asp443_Lys479del)]

Type of variant DNA

Substitution

Type of variant RNA

Substitution/ Splicing (splice donor site)

Type of variant Protein

Substitution (silent)

ACMG classification

Likely pathogenic

Predicted severity

Less severe

Phenotype with null allele

Unknown (disease-associated)

CRIM status

Positive

MAF

MAF not reported

Biochemical evidence of pathogenicity

gives 1,2% residual activity in expression study - causes exon 9 skip

Splicing and translation prediction

weakens exon 9 splice donor

Biochemical evidence of CRIM status

detection of leaky wildtype splicing

Prediction of CRIM status

unknown

Missense prediction (Mutation Taster)

Disease causing (p-value: 0.998)

Missense prediction (SIFT)

Tolerated (score: 0.06)

Missense prediction (Align GVGD)

Class C25 (GV: 32.40 - GD: 65.72)

The Pompe disease GAA variant database represents an effort to collect all known variants in the GAA gene and is maintained and provide by the Pompe center, Erasmus MC.

We kindly ask you to reference one of the following articles if you use this database for research purposes:

de Faria, DOS, in 't Groen, SLM, Bergsma, AJ, et al. Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening.
Human Mutation. 2021; 42: 119-134. https://doi.org/10.1002/humu.24148

Niño, MY, in 't Groen, SLM, Hoogeveen-Westerveld, M, et al. Extension of the Pompe mutation database by linking disease‐associated variants to clinical severity. Human Mutation. 2019; 40: 1954–1967. https://doi.org/10.1002/humu.23854

www.pompecenter.nl