rs10425935 (VSTM2B-DT): Brain Expression Variant
Key takeaways
- This variant reduces expression of VSTM2B-DT, a non-coding RNA gene, in at least three cortical brain regions.
- It was studied in a genome-wide association study of obesity-related traits in 815 Hispanic children.
- Evidence is preliminary, with no independent replication reported in the available sources.
- No drug response or clinical annotation data are currently available for this variant.
Key takeaways
- This variant reduces expression of VSTM2B-DT, a non-coding RNA gene, in at least three cortical brain regions.
- It was studied in a genome-wide association study of obesity-related traits in 815 Hispanic children.
- Evidence is preliminary, with no independent replication reported in the available sources.
- No drug response or clinical annotation data are currently available for this variant.
What the research says A genome-wide association study of 1.1 million SNPs in 815 Hispanic children from the VIVA LA FAMILIA Study examined a broad range of obesity-related phenotypes - including anthropometry, body composition, diet, energy expenditure, hormones, and inflammation - to identify genetic variants influencing childhood obesity and its comorbidities. Expression-quantitative trait locus (eQTL) data from GTEx v11, based on 953 donors with cis-window analysis at FDR less than 0.05, show that the alternate allele at this locus is associated with reduced expression of VSTM2B-DT - a divergent transcript (a long non-coding RNA gene transcribed in the opposite direction from the overlapping VSTM2B protein-coding gene) - in three cortical brain regions, with the strongest effect in the anterior cingulate cortex. GTEx Portal
Reported associations
- VSTM2B-DT expression in anterior cingulate cortex (BA24): The alternate allele is associated with reduced expression of this non-coding RNA in the anterior cingulate cortex, a frontal brain region involved in cognition and emotional processing (p=5.6e-7). GTEx Portal
- VSTM2B-DT expression in cortex: Reduced expression of the same gene is observed in general cortical tissue with the alternate allele (p=6.8e-7). GTEx Portal
- VSTM2B-DT expression in frontal cortex (BA9): The alternate allele is also associated with reduced expression in the dorsolateral prefrontal cortex, representing the smallest of the three eQTL effects (p=5.3e-5). GTEx Portal
- Childhood obesity-related traits: This variant was included in a GWAS of Hispanic children (n=815) covering traits such as weight, body composition, metabolites, hormones, diet, and energy expenditure; specific association results for rs10425935 are not described in the available study text.
Evidence quality The eQTL associations are drawn from GTEx v11 (953 donors), with all three effects passing the FDR less than 0.05 threshold: anterior cingulate cortex BA24 (p=5.6e-7, log2-normalized slope=-0.45), cortex (p=6.8e-7, slope=-0.37), and frontal cortex BA9 (p=5.3e-5, slope=-0.33). GTEx Portal The VIVA LA FAMILIA childhood obesity GWAS (815 Hispanic children across 263 families, 1.1 million SNPs genotyped) provides broader biological context for the region, but the available study text does not report specific findings for rs10425935; any link between this variant and obesity phenotypes must therefore be treated as preliminary and unconfirmed. No independent replication of any association at this locus is described in the provided sources, and the overall evidence base is limited.
Tissue-specific expression effects
- VSTM2B-DT: The alternate allele is associated with reduced expression in three brain regions - the anterior cingulate cortex (BA24), the general cortex, and the frontal cortex (BA9). All three effects represent decreased rather than increased expression, with the strongest reduction observed in the anterior cingulate cortex. GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is VSTM2B-DT?
VSTM2B-DT is a divergent transcript - a type of non-coding RNA gene that runs in the opposite direction from the nearby VSTM2B protein-coding gene. Non-coding RNAs do not produce proteins but can help regulate gene activity in surrounding regions.
What does rs10425935 do to gene expression?
Based on GTEx data from 953 donors, the alternate allele at rs10425935 is associated with reduced expression of VSTM2B-DT in three brain regions: the anterior cingulate cortex, the cortex, and the frontal cortex. This is a gene expression effect, not a direct measure of any health outcome.
Is rs10425935 linked to childhood obesity?
This variant was included in a genome-wide association study of childhood obesity traits in Hispanic children, but specific association results for rs10425935 are not described in the available research. Any link to obesity phenotypes remains unconfirmed.
Which brain regions are affected by rs10425935?
GTEx data show reduced VSTM2B-DT expression in the anterior cingulate cortex (BA24), the general cortex, and the frontal cortex (BA9). These are regions involved in attention, cognition, and decision-making, though the functional consequences of changes in non-coding RNA expression in these areas are not yet established.
What population was rs10425935 studied in?
This variant was examined in the VIVA LA FAMILIA Study, a genome-wide association study of 815 Hispanic children from 263 families in Houston, Texas. The study focused on childhood obesity and a wide range of related biological traits.