rs2815752 — NEGR1

Top obesity GWAS variant near NEGR1 — affects hypothalamic appetite regulation and neuronal growth

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Your Brain's Appetite Thermostat — NEGR1 and Obesity Risk

NEGR1 (Neuronal Growth Regulator 1) encodes a GPI-anchored cell adhesion molecule11 GPI-anchored cell adhesion molecule
Glycosylphosphatidylinositol — a lipid anchor that attaches proteins to the outer surface of cell membranes belonging to the IgLON family. It is strongly expressed in the hypothalamus — the brain region that governs hunger, satiety, and energy balance. The rs2815752 variant sits upstream of NEGR1 and alters its expression, making it one of the first obesity-associated genes identified by genome-wide association studies that pointed to a neuronal, rather than metabolic, mechanism for weight gain.

The Mechanism

NEGR1 promotes neurite outgrowth, synapse formation, and cell-cell adhesion in hypothalamic neurons, particularly in the arcuate nucleus22 arcuate nucleus
The arcuate nucleus contains hunger-promoting (AgRP/NPY) and satiety-promoting (POMC) neurons that integrate signals from hormones like leptin and ghrelin and ventromedial hypothalamus. It accumulates at GABAergic inhibitory synapses and promotes clustering of GAD6533 GAD65
Glutamic acid decarboxylase 65 — the enzyme that synthesizes GABA, the main inhibitory neurotransmitter at synaptic membranes. When NEGR1 expression is reduced — as occurs with the A risk allele — hypothalamic appetite circuits are disrupted: the GABAergic synaptic architecture weakens, and the brain's ability to regulate food intake diminishes.

A linked 45-kb deletion polymorphism upstream of NEGR1 removes several conserved regulatory elements, likely explaining how the common risk haplotype reduces NEGR1 expression. 44 Willer et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat Genet, 2009

The Evidence

The NEGR1 locus was identified in the landmark GIANT consortium GWAS55 GIANT consortium GWAS
Willer et al. Meta-analysis of 15 GWAS for BMI (n>32,000) with replication in 14 cohorts (n>59,000). Nat Genet, 2009 as one of six new BMI loci, with the A allele increasing BMI by 0.10 kg/m2 per copy (P = 6.0 x 10-8, combined n = 83,499). The largest BMI meta-analysis to date (339,224 individuals66 339,224 individuals
Locke et al. Genetic studies of body mass index yield new insights for obesity biology. Nature, 2015) confirmed NEGR1 among 97 genome-wide significant loci and highlighted its central nervous system expression pattern.

Mouse studies validate the human genetics. NEGR1-knockout mice show reduced body mass (8-13%)77 reduced body mass (8-13%)
Lee et al. Functional inactivation of the GWAS obesity gene NEGR1 in mice causes a body mass phenotype. PLOS ONE, 2012, decreased food intake, and reduced lean mass — confirming NEGR1's role in appetite and body composition. In rats, decreased hypothalamic NEGR1 expression88 decreased hypothalamic NEGR1 expression
Boender et al. The obesity-associated gene Negr1 regulates aspects of energy balance in rat hypothalamic areas. Physiol Genomics, 2014 directly increases body weight and food intake, particularly affecting carbohydrate preference.

In a human dietary study of 26,107 participants, the A risk allele was associated with lower fat intake but higher carbohydrate and fiber intake99 A risk allele was associated with lower fat intake but higher carbohydrate and fiber intake
Rukh et al. Genetic susceptibility to obesity and diet intakes in the Malmö Diet and Cancer Study. Genes Nutr, 2013, suggesting NEGR1 influences not just how much we eat but what we prefer to eat.

Practical Actions

Because the A allele is extremely common (carried by 86% of Europeans and over 99% of East Asians as at least one copy), this is not a rare high-impact variant — it is a common, moderate-effect contributor to obesity susceptibility. The practical value lies in understanding your position on the appetite regulation spectrum.

Carriers of two A alleles should focus on structured meal timing and protein-forward meals to support satiety signaling that their hypothalamic wiring handles less efficiently. Monitoring waist circumference rather than just body weight captures the metabolic risk more accurately.

Interactions

NEGR1 contributes to a polygenic obesity risk profile alongside FTO (rs9939609) and MC4R (rs17782313). While each variant has a modest individual effect, carrying risk alleles at multiple loci has a cumulative impact on BMI. A combined FTO + NEGR1 risk genotype may warrant more structured appetite management strategies than either alone.

NEGR1 is also a cross-trait hit for major depressive disorder, with integrative genomic analysis1010 integrative genomic analysis
Li et al. Integrating GWAS and eQTL data identifies NEGR1 as a causal risk gene of major depression. J Affect Disord, 2020 identifying it as a causal MDD risk gene. The shared neurodevelopmental mechanism — disrupted synaptic connectivity in hypothalamic and limbic circuits — may explain why obesity and depression so often co-occur. Carriers of the A allele at rs2815752 who also carry depression-associated variants may experience compounded effects on both appetite regulation and mood.

Nutrient Interactions

dietary carbohydrates altered_metabolism
dietary fat altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

GG Robust Appetite Control Normal

No risk alleles — intact hypothalamic appetite regulation

You carry two copies of the protective G allele at rs2815752. Only about 14% of Europeans have this genotype — you are in the minority with the most robust NEGR1 expression in the hypothalamus.

Your appetite regulation circuitry functions at full capacity. NEGR1 maintains normal GABAergic synaptic architecture in your arcuate nucleus and ventromedial hypothalamus, supporting efficient satiety signaling after meals. This does not make you immune to weight gain from environmental factors, but your neurological appetite thermostat is set at its most effective.

AG Moderate Appetite Risk Intermediate

One risk allele — mildly reduced appetite regulation

The AG genotype produces an intermediate level of NEGR1 in hypothalamic neurons. You retain partial GABAergic synaptic function in the arcuate nucleus and ventromedial hypothalamus, meaning your satiety signaling is mildly impaired but still largely functional.

The Malmö Diet and Cancer Study (n = 26,107) showed that each A allele shifts macronutrient preference slightly toward carbohydrates and away from fat. This effect is smaller in heterozygotes than AA homozygotes, consistent with the additive inheritance pattern.

As a heterozygote, your obesity risk from this single locus is modest. However, if you carry risk alleles at other obesity-associated genes (FTO, MC4R), the combined effect may be more substantial.

AA Appetite Dysregulated High Risk

Two risk alleles — reduced hypothalamic appetite control

The AA genotype at rs2815752 results in the lowest NEGR1 expression levels. NEGR1 is a GPI-anchored IgLON family cell adhesion molecule critical for maintaining GABAergic synaptic architecture in the arcuate nucleus and ventromedial hypothalamus — the brain regions that integrate hunger and satiety signals from leptin, ghrelin, and insulin.

With reduced NEGR1, GAD65 clustering at synaptic membranes is impaired, weakening inhibitory tone in appetite circuits. The functional consequence is diminished satiety signaling — it takes more food to feel full, and fullness dissipates faster.

NEGR1 knockout mice show 8-13% reduced body mass with decreased food intake and reduced lean mass, while rats with hypothalamic NEGR1 knockdown gain weight through increased food consumption. The human dietary data from the Malmö study (n = 26,107) confirms that A allele carriers shift macronutrient preference toward carbohydrates and away from fat.

NEGR1 is also one of the strongest cross-trait hits linking obesity and major depression through shared synaptic connectivity pathways, suggesting that carriers may experience intertwined effects on both appetite and mood regulation.