--- title: "GLA P409A (c.1225C>G, rs878853698) | Dante Labs" description: "ClinVar classifies GLA P409A as Pathogenic (criteria provided, multiple submitters, no conflicts). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/gla/variants/p409a" --- 1. [Genes](https://dantelabs.com/genes) 2. [GLA](https://dantelabs.com/genes/gla) 3. GLA P409A Variant # GLA P409A NM_000169.3(GLA):c.1225C>G (p.Pro409Ala) Also known as - p.Pro409Ala - p.P409A - rs878853698 * ClinVar classification Pathogenic * Review status 2 stars out of 4 criteria provided, multiple submitters, no conflicts * Last evaluated 8 September 2026 Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.19-9814e911 Facts last changed 18 October 2026 ## Summary P409A is a missense variant in GLA: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as pathogenic for Fabry Disease (criteria provided, multiple submitters, no conflicts). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | --------------------------------------------------------------------- | ------------- | ---------------- | | [Fabry Disease](https://dantelabs.com/conditions/fabry-disease) [ClinVar VCV000495691 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/495691/) | Pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | 2 submissions | 8 September 2026 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## ACMG/AMP criteria The ACMG/AMP criteria P409A meets, from its predicted effect in GLA, gnomAD and ClinVar. | Criterion | Strength | Rests on | | ----------------------------------------------- | ---------- | -------------------------------------------------------------------------- | | PM2 Absent or very rare in population databases | Supporting | Not seen in gnomAD exomes, gnomAD genomes | | PP5 A reputable source reports it as pathogenic | Supporting | ClinVar: Pathogenic (criteria provided, multiple submitters, no conflicts) | On these criteria alone: uncertain significance. Assessed automatically, without functional, computational or family evidence. Not a clinical classification. ## Population frequency How often P409A is seen among the people whose exomes and genomes gnomAD 4.1 brings together. | Dataset | Allele frequency | Allele count | Homozygotes | Commonest in | | -------------- | ---------------- | ------------ | ----------- | ------------ | | gnomAD exomes | Not seen | 0 of 0 | 0 | | | gnomAD genomes | Not seen | 0 of 0 | 0 | | Figures from gnomAD 4.1, as gnomAD publishes them. Groups are genetic ancestry groups as gnomAD infers them. They describe the variant in gnomAD's populations, not anyone's result. [P409A in the gnomAD browser (opens in a new tab)](https://gnomad.broadinstitute.org/variant/X-101397874-G-C?dataset=gnomad_r4) ## Where it lies in GLA P409A lies in exon 7 of the 7 in GLA's MANE Select transcript, NM_000169.3. [GLA variants in exon 7 →](https://dantelabs.com/genes/gla/variants?exon=7) [GLA's gene diagram →](https://dantelabs.com/genes/gla#gene-structure) ## Molecular details | Gene | [GLA](https://dantelabs.com/genes/gla) | | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000169.3 MANE Select | | Coding DNA change (HGVS c.) | c.1225C>G | | Protein change (HGVS p.) | p.Pro409Ala p.P409A | | Predicted consequence | Missense [missense_variant (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001583) | | Predicted impact | Moderate | | Position (GRCh38) | chrX:101397874 G>C | | Position (GRCh37) | chrX:100652862 G>C | | dbSNP ID | [rs878853698 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs878853698) | | ClinVar Variation ID | [VCV000495691 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/495691/) | | ClinVar Allele ID | 488021 | | ClinGen Allele Registry ID | [CA413919170 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA413919170) | | ClinVar name | NM_000169.3(GLA):c.1225C>G (p.Pro409Ala) | ## GLA P409A in other databases - [ClinVar VCV000495691 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/495691/) - [dbSNP rs878853698 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs878853698) - [ClinGen Allele Registry CA413919170 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA413919170) - [gnomAD X-101397874-G-C (opens in a new tab)](https://gnomad.broadinstitute.org/variant/X-101397874-G-C?dataset=gnomad_r4) - [Ensembl rs878853698 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs878853698) ## Reports that look at this variant (2) These Genome Test condition reports include P409A among the variants they look at. | Report | Conditions | Inheritance | | --------------------------------------------------------------------------------------- | ------------------------------------------------------- | ------------------ | | [Fabry Disease](https://dantelabs.com/conditions/fabry-disease) | Fabry Disease | X-linked recessive | | [Lysosomal Storage Disease](https://dantelabs.com/conditions/lysosomal-storage-disease) | Lysosomal storage disease (other and unspecified types) | | ## Other variants in GLA - [A15E Pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a15e) - [A20D Pathogenic/likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a20d) - [A20Gfs\*2 Pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a20gfs2) - [A29Gfs\*2 Pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a29gfs2) - [A31V Likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a31v) - [A37P Pathogenic/likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a37p) - [A37T Likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a37t) - [A97V Pathogenic/likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a97v) - [A121P Likely pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a121p) - [A135V Pathogenic 2 stars out of 4](https://dantelabs.com/genes/gla/variants/a135v) [All GLA variants](https://dantelabs.com/genes/gla/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 2026-10-19-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-19). - 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 2026.10.19-9814e911 of 19 October 2026. ## Cite this page APA > Dante Labs. (18 October 2026). GLA P409A (c.1225C>G, rs878853698) (Version 2026.10.19-9814e911). Retrieved 20 October 2026, from https\://dantelabs.com/genes/gla/variants/p409a Vancouver > Dante Labs. GLA P409A (c.1225C>G, rs878853698) \[Internet]. Version 2026.10.19-9814e911. 18 October 2026 \[cited 20 October 2026]. Available from: https\://dantelabs.com/genes/gla/variants/p409a Download citation [RIS](https://dantelabs.com/genes/gla/variants/p409a/cite.ris) [BibTeX](https://dantelabs.com/genes/gla/variants/p409a/cite.bib) [CSL-JSON](https://dantelabs.com/genes/gla/variants/p409a/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)