Variant
GAA S529V
NM_000152.5(GAA):c.1585_1586delinsGT (p.Ser529Val)
- p.Ser529Val
- p.S529V
- rs121907941
- ClinVar classification
- Likely pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 17 June 2025
- 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-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
S529V is a missense variant in GAA: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as likely 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)ClinVar VCV000004026 (opens in a new tab) | Likely pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 17 June 2025 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in GAA
S529V lies in exon 11 of the 20 in GAA's MANE Select transcript, NM_000152.5.
Molecular details
| Gene | GAA |
|---|---|
| Transcript | NM_000152.5MANE Select |
| Coding DNA change (HGVS c.) | c.1585_1586delinsGT |
| Protein change (HGVS p.) | p.Ser529Valp.S529V |
| Predicted consequence | Missensemissense_variant (opens in a new tab) |
| Predicted impact | Moderate |
| Position (GRCh38) | chr17:80110974 TC>GT |
| Position (GRCh37) | chr17:78084773 TC>GT |
| dbSNP ID | rs121907941 (opens in a new tab) |
| ClinVar Variation ID | VCV000004026 (opens in a new tab) |
| ClinVar Allele ID | 19065 |
| ClinGen Allele Registry ID | CA116604 (opens in a new tab) |
| ClinVar name | NM_000152.5(GAA):c.1585_1586delinsGT (p.Ser529Val) |
GAA S529V in other databases
Reports that look at this variant (2)
These Genome Test condition reports include S529V among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Lysosomal Storage Disease | Lysosomal storage disease (other and unspecified types) | |
| Pompe Disease | Pompe Disease (Glycogen Storage Disease II) | Autosomal recessive |
Other variants in GAA
- A14Rfs*18Pathogenic3 stars out of 4
- A150Gfs*27Likely pathogenic3 stars out of 4
- A382Lfs*10Pathogenic3 stars out of 4
- A486PLikely pathogenic3 stars out of 4
- A610Dfs*88Pathogenic3 stars out of 4
- A691Sfs*7Pathogenic3 stars out of 4
- A761Ifs*35Pathogenic3 stars out of 4
- c.-32-1G>CLikely pathogenic3 stars out of 4
- c.-32-2A>GLikely pathogenic3 stars out of 4
- c.-32-3C>APathogenic3 stars out of 4
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
Dante Labs. (16 October 2026). GAA S529V (c.1585_1586delinsGT, rs121907941) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/gaa/variants/s529v
Dante Labs. GAA S529V (c.1585_1586delinsGT, rs121907941) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/gaa/variants/s529v
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