rs31489
A SNP in the CLPTM1L gene on chromosome 5. Its most notable genotype is A;C: 1.75-fold reduced risk of developing lung cancer
- Gene
- CLPTM1L
- Location
- Chr 51,342,599 (GRCh38)
- Highest magnitude
- 2.0Worth knowing
- Tested on
- 23andMe, AncestryDNA
- Minor allele frequency
- 35%
Genotypes
As shown in 23andMe and AncestryDNA files.
- A;ANot ratedReduced lung cancer risk?
- A;CMost notableGood1.75-fold reduced risk of developing lung cancer
- C;CBadIncreased risk for lung cancer and emphysema
On SNPedia: (A;A), (A;C), (C;C). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.
Frequency
Share of each genotype in 11 HapMap populations.
- AverageA;A 11% A;C 40% C;C 49%
- European ancestry (Utah)A;A 16% A;C 46% C;C 38%
- Han Chinese (Beijing)A;A 2% A;C 28% C;C 70%
- Japanese (Tokyo)A;A 2% A;C 22% C;C 76%
- Yoruba (Nigeria)A;A 31% A;C 50% C;C 19%
- African ancestry (Southwest US)A;A 19% A;C 49% C;C 32%
- Chinese (Denver)A;A 3% A;C 28% C;C 70%
- Gujarati IndianA;A 2% A;C 30% C;C 68%
- Luhya (Kenya)A;A 16% A;C 49% C;C 35%
- Mexican ancestry (Los Angeles)A;A 2% A;C 38% C;C 60%
- Maasai (Kenya)A;A 16% A;C 45% C;C 39%
- TuscanA;A 11% A;C 58% C;C 31%
Related
Conditions, medicines and genes
Notes
From SNPedia
Show notes, about 160 words
A;C
The frequency of the minor allele A of rs31489 was 32.49% in cancer patients versus 45.79% in disease-free subjects. Subjects carrying one copy of minor allele A are at 1.75-fold reduced risk of developing lung cancer.
C;C
The rs31489 C-allele correlated with reduced forced expiratory volume in 1 s (p=0.006). Homozygous carriers of the rs31489 C-allele exhibited increased susceptibility to bronchial obstruction (OR 1.82, 95% CI 1.24–2.69; p=0.002). A similar association was observed for diffusing capacity of the lung for carbon monoxide (p=0.004). Consistent with this, CC-carriers had an increased risk of emphysema (OR 2.04, 95% CI 1.41–2.94; p=1.73×10−4) and displayed greater alveolar destruction. Finally, CC-carriers also had an increased risk for lung cancer (OR 1.90, 95% CI 1.21–2.99; p=0.005), and were more susceptible to developing both lung cancer and bronchial obstruction than lung cancer alone (OR 2.11, 95% CI 1.04–4.26; p=0.038).
Source and license
Adapted from rs31489 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.