rs13407913 — ADCY3

Intronic variant in the adenylyl cyclase 3 gene, which encodes a cAMP-producing enzyme essential for hypothalamic ciliary signaling that regulates appetite and body weight

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ADCY3 — The Ciliary Satiety Signal

Inside the neurons that govern hunger and body weight in the hypothalamus, a tiny hair-like structure called the primary cilium11 primary cilium
A single immotile antenna-like projection found on most cells, used for signal reception rather than movement; distinct from motile cilia in airways serves as the master receiver for satiety hormones. The ADCY3 gene encodes adenylyl cyclase 322 adenylyl cyclase 3
An enzyme embedded in the ciliary membrane that converts ATP into cyclic AMP (cAMP), a second messenger that amplifies hormonal signals from leptin, melanocortins, and other satiety factors, a critical signal amplifier that translates incoming satiety messages into cellular responses that suppress appetite and increase energy expenditure. rs13407913 is a common intronic variant in ADCY3 sitting within the broader ADCY3-DNAJC27 genomic locus that has been linked to body mass index across multiple large GWAS studies.

The Mechanism

ADCY3 is selectively concentrated in the primary cilia of hypothalamic neurons, including those in the arcuate, ventromedial, paraventricular, and suprachiasmatic nuclei — the core appetite-regulating regions of the brain. When leptin or melanocortin-4 receptor (MC4R)33 melanocortin-4 receptor (MC4R)
A G-protein-coupled receptor in hypothalamic neurons activated by the satiety peptide alpha-MSH, signaling fullness and suppressing food intake agonists activate their respective G-protein-coupled receptors on ciliary membranes, ADCY3 generates cAMP within the cilium. This local cAMP pulse drives intracellular signaling cascades that reduce food intake and promote energy expenditure.

Loss-of-function mutations in ADCY3 — whether engineered in mice, naturally occurring in Greenlandic Inuit populations (splice variant c.2433-1G>A), or identified in rare variant screens of diverse ancestries — consistently produce severe obesity. The mechanism is failure of hypothalamic neurons to properly transduce satiety signals: hormones bind and receptors activate, but without ADCY3 in the cilium, the cAMP pulse that would normally dampen appetite does not occur. The c.2433-1G>A splice variant44 c.2433-1G>A splice variant
Disrupts a splice acceptor site, causing exon skipping and intron retention, reducing overall ADCY3 RNA and protein expression in carriers found in Greenlandic Inuit was among the first human loss-of-function variants shown to markedly increase obesity risk through this ciliary pathway.

rs13407913 is an intronic variant located at position c.676-2056 in the ADCY3 transcript — approximately 2,056 nucleotides from exon 676. Intronic variants at this distance from exon boundaries rarely affect splicing directly, but may influence gene expression through regulatory element effects or linkage with other functional variants in the region. The ADCY3-DNAJC27 locus55 ADCY3-DNAJC27 locus
A genomic region on chromosome 2p23.3 containing ADCY3 and the adjacent chaperone gene DNAJC27; methylation changes at this locus suppress expression of both genes, increasing BMI risk has been robustly associated with BMI across populations.

The Evidence

The first functional human evidence came from a childhood GWAS by Stergiakouli et al. 201466 Stergiakouli et al. 2014
Genome-wide association study of height-adjusted BMI in childhood identifies functional variant in ADCY3. Obesity (Silver Spring), 2014; n=5,809 children from ALSPAC, replicated in Generation R which identified a missense variant at the ADCY3 locus (rs11676272) strongly associated with height-adjusted BMI (0.28 kg/m³·¹ per G allele, p = 6 × 10⁻⁹), driven by an expression QTL: the risk allele correlates with reduced ADCY3 mRNA levels. This established that common ADCY3 variation affects gene expression and child BMI.

The biological case was strengthened by Grarup et al. 201877 Grarup et al. 2018
Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nature Genetics, 2018; Greenlandic cohort with replication across trans-ancestry groups, which identified the Greenlandic splice variant (c.2433-1G>A) as markedly increasing obesity and type 2 diabetes risk by disrupting ADCY3 RNA expression. The paper also found enrichment of rare ADCY3 loss-of-function variants among T2D cases in trans-ancestry cohorts, supporting a causal role across populations. A review by Andersen & Hansen 201888 Andersen & Hansen 2018
Genetics of metabolic traits in Greenlanders: lessons from an isolated population. J Intern Med, 2018 confirmed the mechanism: reduced ADCY3 function causes obesity through disrupted primary cilia signaling in the hypothalamus.

Cross-species evidence is consistent: ADCY3-deficient mice are obese, and a 2023 study in Labrador Retrievers identified an intronic ADCY3 deletion associated with 5.56 kg higher body weight per allele99 5.56 kg higher body weight per allele
Among the largest per-allele weight effects ever mapped in a canine GWAS, showing that ADCY3 dosage effects on body weight are conserved across mammals.

For rs13407913 specifically, no published study has reported an independent association or functional characterization of this intronic variant. It resides within the ADCY3 gene and likely tags nearby functional variation through linkage disequilibrium. The population frequency pattern — G allele much more common in Africans (~79%) than Europeans (~43%) — suggests ancestral diversity and population differentiation that could reflect local selection on ADCY3 expression levels.

Practical Actions

ADCY3 function in hypothalamic cilia is central to how your brain registers fullness after meals. When ADCY3-mediated cAMP signaling is reduced, satiety hormones (leptin, alpha-MSH) bind their receptors but the downstream signal is attenuated — appetite suppression is weaker and the drive to eat persists longer than it should. This is a central mechanism, distinct from insulin resistance or adipose tissue thermogenesis deficits.

For carriers of the G allele at rs13407913, the practical implications are modest and uncertain at the level of this specific variant. The broader ADCY3 biology, however, points to two strategies: supporting ciliary signaling through adequate sleep (cilia are most functional in well-rested hypothalamic neurons), and reducing environmental factors that blunt leptin sensitivity (chronic sleep deprivation, ultra-processed food palatability signals). Emerging evidence also suggests that GLP-1 receptor agonists may partially bypass the ciliary cAMP step in hypothalamic satiety signaling.

Interactions

rs13407913 is within the same gene as rs11676272, the missense variant that drives the established ADCY3 BMI association. Whether rs13407913 is in LD with rs11676272 or represents an independent signal has not been determined in published literature.

ADCY3 ciliary signaling intersects with the leptin receptor pathway (LEPR, rs1137101) — a dysfunctional leptin receptor reduces the upstream signal that ADCY3 would amplify, and impaired ADCY3 reduces the ability to transduce even a normal leptin signal. The functional overlap is biological rather than a documented statistical interaction.

The FTO locus (rs9939609) affects adipocyte thermogenesis via IRX3/IRX5, a distinct mechanism from ADCY3's hypothalamic ciliary role. Individuals carrying risk alleles at both loci would face both peripheral (reduced thermogenesis) and central (impaired satiety signaling) contributors to positive energy balance.

Genotype Interpretations

What each possible genotype means for this variant.

AA Standard ADCY3 Activity Normal

Two reference alleles — standard ADCY3 expression and hypothalamic ciliary cAMP signaling

You carry two copies of the reference A allele at rs13407913. This genotype is associated with normal ADCY3 expression in the ADCY3-DNAJC27 locus, supporting standard cAMP signaling in hypothalamic primary cilia that mediate leptin and melanocortin satiety responses. Approximately 32% of people of European descent share this genotype.

AG Intermediate ADCY3 Activity Intermediate

One G allele — potentially reduced ADCY3 expression at this locus; modest increase in BMI predisposition

As a heterozygote, you carry one copy of the allele that marks the ADCY3-DNAJC27 locus for reduced ADCY3 expression. Expression QTL data from the ADCY3 locus suggest the G allele at the lead SNP (rs11676272, a missense variant) correlates with lower ADCY3 RNA, and rs13407913 may be in linkage disequilibrium with this functional variant. The childhood GWAS by Stergiakouli et al. 2014 found 0.28 kg/m³ higher BMI per allele at the lead ADCY3 locus SNP. The biology of ADCY3 in hypothalamic primary cilia — and the dramatic effects of partial or complete loss-of-function in mice, humans, and dogs — establish ADCY3 dosage as mechanistically plausible for modest BMI effects at the common variant level.

Critically, the evidence for rs13407913 specifically is emerging: the variant is not cited independently in the published literature and its LD with functional ADCY3 variants has not been formally reported.

GG Reduced ADCY3 Activity Decreased

Two G alleles — likely reduced ADCY3 expression at this locus with potential impairment of hypothalamic satiety signaling

Homozygous GG carriers at rs13407913 sit at the higher-risk end of the common ADCY3 variant spectrum. The mechanistic chain runs: two G alleles → potentially lower ADCY3 expression at the locus level → reduced cAMP production in hypothalamic primary cilia → blunted transduction of leptin and MC4R satiety signals → tendency toward higher food intake and positive energy balance.

The Stergiakouli et al. 2014 childhood GWAS (n=5,809 ALSPAC participants) found 0.28 kg/m³ per allele at the ADCY3 lead SNP, meaning GG homozygotes would be expected to have roughly double the per-allele effect (~0.56 kg/m³ higher height-adjusted BMI) compared to AA homozygotes. These are common variant effect sizes — meaningful in aggregate, not deterministic individually.

The type 2 diabetes risk at the ADCY3 locus parallels its BMI association: Grarup et al. 2018 found that ADCY3 loss-of-function variants increase T2D risk beyond their effect on BMI, consistent with a direct role of ADCY3-mediated cAMP signaling in pancreatic beta-cell function and insulin secretion in addition to its hypothalamic satiety role.

Note: the elevated G allele frequency in Africans (~79%) suggests this allele has ancient roots and does not carry the same BMI risk signal in that population context — ancestral environment and haplotype background matter.