rs10990645 (LINC01492): Vaginal Microbiome Variant

Key takeaways

• rs10990645, located near LINC01492, was among 72 variants significantly associated with vaginal bacterial community traits in pregnant women at genome-wide significance
• The vaginal bacteriome study was conducted in a cohort of 359 pregnant Chinese women using 16S rRNA bacteriome analysis
• GTEx data from 953 donors links this variant to reduced LINC01492 gene expression specifically in testis tissue
• Vaginal bacteriome evidence is preliminary: a single small cohort with no reported replication in other populations

What the research says A genome-wide association study of vaginal bacterial traits in 359 pregnant Chinese women identified 72 host genetic variant associations at genome-wide significance (P < 5 x 10^-8), most carrying low minor allele frequencies (MAF below 0.05). GTEx v11 eQTL data from 953 donors shows that the alternate allele at rs10990645 is associated with reduced expression of the gene in testis tissue (slope -0.11, p = 2.0 x 10^-6, FDR < 0.05) GTEx Portal.

Reported associations

• Vaginal bacterial trait composition (pregnant women): rs10990645 was identified in a GWAS of vaginal bacterial community traits conducted in 359 pregnant Chinese women; the study found 72 host genetic variants associated at genome-wide significance (P < 5 x 10^-8), though the specific bacterial taxon linked to this variant is not detailed in the provided study excerpt
• LINC01492 testis expression (eQTL): The alternate allele is associated with reduced expression of the gene in testis tissue (slope -0.11, p = 2.0 x 10^-6) GTEx Portal

Evidence quality The vaginal bacteriome association derives from a single cohort study of 359 pregnant Chinese women using 16S rRNA gene-targeted bacteriome analysis. The study reported an acceptable genomic inflation factor (lambda < 1.1), which reduces concern about spurious signals from population stratification, but no independent replication in other cohorts is reported in the available literature, so this finding is considered preliminary. The no-PMID study metadata also limits inline citation traceability for this signal. The testis eQTL signal from GTEx v11 is based on 953 donors and reaches the FDR < 0.05 threshold (p = 2.0 x 10^-6) GTEx Portal, providing a more robustly powered mechanistic observation; however, eQTL effects reflect gene expression regulation and do not directly imply clinical outcomes.

Tissue-specific expression effects

• LINC01492: Reduced expression in testis tissue is associated with the alternate allele; no other tissues reached significance in the available GTEx data GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.