--- title: "GAA E656del (c.1962_1964del, rs1030961946) | Dante Labs" description: "ClinVar classifies GAA E656del as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/gaa/variants/e656del" --- 1. [Genes](https://dantelabs.com/genes) 2. [GAA](https://dantelabs.com/genes/gaa) 3. GAA E656del Variant # GAA E656del NM_000152.5(GAA):c.1962_1964del (p.Glu656del) Also known as - p.Glu656del - p.E656del - rs1030961946 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 5 May 2020 * Expert panel ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bf Facts last changed 16 October 2026 ## Summary E656del is an in-frame variant in GAA: it adds or removes one or more amino acids without shifting how the rest of the gene's code is read. ClinVar classifies it as pathogenic for Pompe Disease (Glycogen Storage Disease II) (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | -------------- | | [Pompe Disease (Glycogen Storage Disease II)](https://dantelabs.com/conditions/pompe-disease) [ClinVar VCV000932896 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/932896/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 5 May 2020 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## Where it lies in GAA E656del lies in exon 14 of the 20 in GAA's MANE Select transcript, NM_000152.5. [GAA variants in exon 14 →](https://dantelabs.com/genes/gaa/variants?exon=14) [GAA's gene diagram →](https://dantelabs.com/genes/gaa#gene-structure) ## Molecular details | Gene | [GAA](https://dantelabs.com/genes/gaa) | | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000152.5 MANE Select | | Coding DNA change (HGVS c.) | c.1962_1964del | | Protein change (HGVS p.) | p.Glu656del p.E656del | | Predicted consequence | In-frame insertion or deletion [disruptive_inframe_deletion (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001826) | | Predicted impact | Moderate | | Position (GRCh38) | chr17:80112948 CAGA>C | | Position (GRCh37) | chr17:78086747 CAGA>C | | dbSNP ID | [rs1030961946 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs1030961946) | | ClinVar Variation ID | [VCV000932896 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/932896/) | | ClinVar Allele ID | 921205 | | ClinGen Allele Registry ID | [CA294896907 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA294896907) | | ClinVar name | NM_000152.5(GAA):c.1962_1964del (p.Glu656del) | ## GAA E656del in other databases - [ClinVar VCV000932896 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/932896/) - [dbSNP rs1030961946 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs1030961946) - [ClinGen Allele Registry CA294896907 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA294896907) - [gnomAD 17-80112948-CAGA-C (opens in a new tab)](https://gnomad.broadinstitute.org/variant/17-80112948-CAGA-C?dataset=gnomad_r4) - [Ensembl rs1030961946 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs1030961946) ## Reports that look at this variant (2) These Genome Test condition reports include E656del among the variants they look at. | Report | Conditions | Inheritance | | --------------------------------------------------------------------------------------- | ------------------------------------------------------- | ------------------- | | [Lysosomal Storage Disease](https://dantelabs.com/conditions/lysosomal-storage-disease) | Lysosomal storage disease (other and unspecified types) | | | [Pompe Disease](https://dantelabs.com/conditions/pompe-disease) | Pompe Disease (Glycogen Storage Disease II) | Autosomal recessive | ## Other variants in GAA - [A14Rfs\*18 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a14rfs18) - [A150Gfs\*27 Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a150gfs27) - [A382Lfs\*10 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a382lfs10) - [A486P Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a486p) - [A610Dfs\*88 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a610dfs88) - [A691Sfs\*7 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a691sfs7) - [A761Ifs\*35 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/a761ifs35) - [c.-32-1G>C Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/c--32-1g-c) - [c.-32-2A>G Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/c--32-2a-g) - [c.-32-3C>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/gaa/variants/c--32-3c-a) [All GAA variants](https://dantelabs.com/genes/gaa/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026. ## Cite this page APA > Dante Labs. (16 October 2026). GAA E656del (c.1962_1964del, rs1030961946) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https\://dantelabs.com/genes/gaa/variants/e656del Vancouver > Dante Labs. GAA E656del (c.1962_1964del, rs1030961946) \[Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 \[cited 16 October 2026]. Available from: https\://dantelabs.com/genes/gaa/variants/e656del Download citation [RIS](https://dantelabs.com/genes/gaa/variants/e656del/cite.ris) [BibTeX](https://dantelabs.com/genes/gaa/variants/e656del/cite.bib) [CSL-JSON](https://dantelabs.com/genes/gaa/variants/e656del/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)