rs1064039

A SNP in the CST3 gene on chromosome 20. Its most notable genotype is T;T: Higher risk for age-related macular degeneration; slightly higher Alzheimers risk in Caucasians but not Asians

Gene
CST3
Location
Chr 2023,637,790 (GRCh38)
Highest magnitude
2.0Worth knowing
Tested on
23andMe
Minor allele frequency
19%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TMost notableBadHigher risk for age-related macular degeneration; slightly higher Alzheimers risk in Caucasians but not AsiansWorth knowing · 2.0
  2. C;TBadslightly higher risk for Alzheimers in Caucasians but not AsiansMinor · 1.2
  3. C;CGoodcommon in clinvarTypical · 0.0

SNPedia records rs1064039 on the minus strand: (A;A), (A;G), (G;G). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Other CST3 SNPs

All CST3 SNPs

Notes

From SNPedia

Show notes, about 160 words

rs1064039, also known as G73A, Ala25Thr or A25T, is a variant in the cystatin C CST3 gene. A relatively small study (167 patients) concluded that rs1064039(A;A) genotypes had about a 3 fold increase in risk for exudative age-related macular degeneration (ARMD). A meta-analysis of 2,410 cases and 2,539 controls reported that although the rs1064039(A) allele is associated with about a 1.5x increased odds ratio for developing Alzheimer's disease in Caucasians, no increased risk was seen in Asians.

T;T

Higher risk (2 or 3 fold, perhaps) for age-related macular degeneration has been reported based on a relatively small study of German patients. In Caucasians but not Asians, a meta-analysis concluded that the (A) allele was associated with about a 1.5x higher risk for Alzheimers in both dominant and recessive models.

C;T

This variant has been reported to be associated with a slightly higher risk for Alzheimers disease in Caucasians but not in Asians.

Source and license

Adapted from rs1064039 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.