rs1841499 — NEGR1

Hypothalamic appetite regulator variant linking obesity susceptibility to migraine risk via shared neural pathways

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The Brain's Appetite Wiring and Its Metabolic Consequences

NEGR1 (Neuronal Growth Regulator 1) encodes a cell-adhesion molecule expressed primarily in the hypothalamus, the brain region that acts as the body's central thermostat for hunger, satiety, and energy expenditure. 11 NEGR1 belongs to the IgLON family of immunoglobulin-domain cell adhesion molecules that regulate neurite outgrowth and synapse formation The rs1841499 variant sits within the NEGR1 locus on chromosome 1p31.1 and was identified as a novel shared risk locus between migraine and type 2 diabetes in a large cross-trait GWAS meta-analysis.

The Mechanism

NEGR1 promotes cell-cell adhesion and neurite growth in hypothalamic neurons that control food intake. The protein is cleaved by the protease ADAM10, activating FGFR2 signaling and promoting neuronal spine plasticity. When NEGR1 function is reduced, hypothalamic circuits governing appetite become dysregulated, leading to increased food intake and body weight gain. 22 In mouse models, NEGR1 knockout leads to increased adiposity, decreased lean mass, and pre-diabetic metabolic changes

The variant's effect on both migraine and metabolic disease likely stems from NEGR1's dual role: it shapes hypothalamic neural architecture (affecting energy balance) while also modulating monoaminergic neurotransmission (dopamine and serotonin pathways implicated in migraine). NEGR1-deficient mice show altered dopamine release in the striatum and upregulation of dopamine and serotonin transporters.

The Evidence

The cross-trait GWAS meta-analysis33 cross-trait GWAS meta-analysis
Siewert-Rocks et al. Genetic Overlap Analysis Identifies a Shared Etiology between Migraine and Headache with Type 2 Diabetes. Genes, 2022 identified rs1841499 at the NEGR1 locus as one of 23 novel shared loci between migraine and type 2 diabetes (P = 2.86 x 10-8), with concordant protective effects for both traits (migraine OR 0.98, T2D OR 0.97 for the A allele).

NEGR1 was originally identified as an obesity gene through large-scale GWAS. Functional studies in mice44 Functional studies in mice
Lee et al. Functional Inactivation of the Genome-Wide Association Study Obesity Gene NEGR1 in Mice. PLOS ONE, 2012 confirmed that NEGR1 inactivation causes significant body mass changes. A rat hypothalamic study55 rat hypothalamic study
Boender et al. The obesity-associated gene Negr1 regulates aspects of energy balance in rat hypothalamic areas. Physiol Genomics, 2014 demonstrated that decreased NEGR1 expression in periventricular hypothalamic areas increases body weight through increased food intake.

The C allele frequency varies dramatically across ancestries: ~38% in Europeans but only ~8% in East Asians and ~47% in Africans, which may contribute to population-level differences in obesity prevalence patterns.

Practical Actions

Carriers of the C allele have a genetically predisposed tendency toward increased appetite drive. While the per-allele effect is modest (consistent with typical GWAS obesity loci), it compounds with other appetite and metabolism variants. The dual migraine-metabolic connection suggests that metabolic interventions supporting stable blood glucose may benefit both conditions.

Interactions

NEGR1 operates in the same hypothalamic appetite-regulation network as other obesity GWAS genes including MC4R and FTO. The variant rs2815752, located ~60 kb upstream of NEGR1, is in the same GWAS locus and may tag partially overlapping regulatory elements. Carriers of risk alleles at multiple appetite-regulation loci may experience compounding effects on satiety signaling.

Nutrient Interactions

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Genotype Interpretations

What each possible genotype means for this variant.

AA Standard Appetite Regulation Normal

Normal NEGR1 function with typical appetite signaling

You carry two copies of the common A allele at this NEGR1 locus. Your hypothalamic appetite-regulation circuitry functions at baseline levels. About 38% of people of European descent share this genotype, though it is much more common in East Asian populations (~85%).

AC Mildly Increased Appetite Drive Intermediate

One copy modestly increases appetite signaling and metabolic risk

The C allele at rs1841499 was identified in a cross-trait GWAS meta-analysis as a shared risk locus between migraine and type 2 diabetes. NEGR1 modulates hypothalamic neurite outgrowth and synaptic connectivity in neurons that regulate food intake. With one copy, you may have a slightly stronger appetite drive compared to AA homozygotes, though environmental factors play a much larger role than this single variant.

CC Elevated Appetite Drive High Risk

Two copies increase appetite signaling and migraine-metabolic risk

NEGR1 homozygous CC carriers have the highest genetic loading at this locus for both migraine susceptibility and type 2 diabetes risk. In animal models, reduced NEGR1 function leads to increased adiposity, decreased lean mass, and pre-diabetic metabolic changes including impaired glucose tolerance. The protein's role in hypothalamic neurite growth and monoaminergic neurotransmission suggests the variant affects both appetite regulation and migraine-relevant neural pathways. The A allele showed concordant protective effects for both migraine (OR 0.98) and T2D (OR 0.97), meaning the C allele confers risk for both conditions.