Expressive

rs11024384 (MYOD1 locus): Vaginal Microbiome GWAS

Key takeaways

  • rs11024384 is near LINC02729 and MYOD1 and was identified as one of 72 variants shaping vaginal bacterial communities in a study of pregnant women
  • The finding comes from a single GWAS of 359 pregnant Chinese women and has not been independently replicated
  • Tissue data show this variant reduces LINC02729 expression in testis and has opposing effects on a nearby gene in skeletal muscle versus testis and pituitary
  • Evidence is preliminary: the minor allele was rare in the study population and no effect size for this specific variant was reported

Key takeaways

  • rs11024384 sits near LINC02729 (a long non-coding RNA gene) and MYOD1, and was flagged in a genome-wide association study (GWAS) of vaginal bacterial community traits in 359 pregnant women
  • That GWAS found 72 host genetic variant associations with vaginal bacterial traits reaching genome-wide significance (p < 5 x 10-8)
  • GTEx tissue data link this variant to reduced LINC02729 expression in testis and to opposing changes in a nearby gene (ENSG00000254586) across skeletal muscle versus testis and pituitary
  • Evidence is preliminary: a single study in one ethnic population with no independent replication reported

What the research says A 2021 GWAS of 359 pregnant Chinese women using 16S rRNA-based bacteriome profiling (a method that identifies bacteria in a sample by sequencing a gene common to all bacteria) found 72 associations between host genetic variants and vaginal bacterial traits (VBTs) at genome-wide significance (p < 5 x 10-8), with a genomic inflation factor (lambda, a quality-control measure indicating how well statistical inflation was controlled) below 1.1; rs11024384 was among the reported associations. The majority of significant variants in that study had a minor allele frequency (MAF, the population proportion of the rarer DNA letter at a given site) below 0.05. Tissue-level expression data from GTEx v11 (953 donors) associate this variant with reduced LINC02729 expression in testis, and with reduced expression of the nearby gene ENSG00000254586 in testis and pituitary but increased expression of that same gene in skeletal muscle GTEx Portal.

Reported associations

  • Vaginal bacterial traits (VBTs) in pregnant women: identified as one of 72 genome-wide significant loci in a GWAS of 359 pregnant Chinese women; the specific bacterial community feature tied to this locus was not detailed in the available study excerpt

Evidence quality The sole phenotypic association evidence comes from a single GWAS of 359 pregnant Chinese women; no effect size specific to rs11024384 was available in the provided study text. The study reported a lambda below 1.1, indicating limited statistical inflation. Most significant hits, including this locus, had MAF values below 0.05, indicating the minor allele was rare in the cohort. No replication cohort or cross-population validation was reported. GTEx eQTL (expression quantitative trait locus, meaning a genetic variant that predicts how much of a gene is expressed in a given tissue) data provide supporting mechanistic context but do not constitute phenotypic replication. Overall, evidence for this locus is preliminary.

Tissue-specific expression effects

  • LINC02729: reduced expression in testis GTEx Portal
  • ENSG00000254586: reduced expression in testis and pituitary; increased expression in skeletal muscle GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs11024384 associated with?

rs11024384 was identified as one of 72 variants linked to vaginal bacterial community traits in pregnant women in a genome-wide association study of 359 participants. Evidence is preliminary and has not been independently replicated.

What does the LINC02729 gene do?

LINC02729 is a long intergenic non-coding RNA gene, a type of gene that does not produce a protein and may play regulatory roles. GTEx tissue data show this variant is linked to reduced LINC02729 expression specifically in testis tissue.

Is rs11024384 linked to the vaginal microbiome during pregnancy?

A 2021 GWAS found rs11024384 among 72 host genetic variants associated with vaginal bacterial traits in pregnant Chinese women. The specific bacterial community feature tied to this variant was not detailed in the available study text.

Does rs11024384 affect gene expression in muscles?

GTEx tissue data show this variant is associated with increased expression of the nearby gene ENSG00000254586 in skeletal muscle, while the same gene shows reduced expression in testis and pituitary tissue. These are tissue-level expression associations and do not by themselves establish clinical outcomes.

How strong is the evidence for rs11024384?

Currently limited to one published GWAS of 359 pregnant Chinese women with no independent replication reported. The variant had a minor allele frequency below 0.05 in that cohort and no specific effect size was provided for this locus in the available text.