Lack of Association of Glutamate Decarboxylase 2 Gene Polymorphisms with Severe Obesity in Utah


  • The costs of publication of this article were defrayed, in part, by the payment of page charges. This article must, therefore, be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Cardiovascular Genetics, 420 Chipeta Way, Room 1160, Salt Lake City, UT 84108. E-mail:


Three polymorphisms of the glutamate decarboxylase 2 gene, which encodes the glutamic acid decarboxylase enzyme, have been associated with severe obesity in a large French cohort. One of these polymorphisms was shown to have functional consequences on promoter expression. Another polymorphism was associated with insulin levels and secretion. These associations were examined in 855 severely obese Utah subjects (mean BMI = 48 kg/m2) and a normal-weight and normoglycemic subset (N = 130, mean BMI = 22 kg/m2) of a random sample of the Utah population (N = 462). Comparisons of the normal-weight random group with the severely obese group did not result in significant genotype or allele frequency differences for any of the three polymorphisms, C61450A, T83897A, or A-243G (all p ≥ 0.18). Haplotypes were also not related to severe obesity (p = 0.10). None of the polymorphisms was significantly related to fasting glucose, insulin levels, or homeostasis model assessment insulin resistance or secretion indices. This study of normal-weight and severely obese subjects from Utah does not provide evidence for involvement of the three genotyped polymorphisms in the glutamate decarboxylase 2 gene with obesity or with insulin- and glucose-related measures associated with obesity.


Severe obesity is highly familial, often begins early in life, and is associated with greatly increased morbidity and mortality (1, 2). Because genetic influences are thought to play a greater role in severe obesity than more moderate obesity, identification of obesity genes may be more easily detected in this group. The glutamate decarboxylase 2 (GAD2)1 gene encoding the glutamic acid decarboxylase enzyme regulates γ-aminobutyric acid, a central nervous system neurotransmitter (3). Despite an early suggestion that GAD2 might be associated with type 1 diabetes (4), a subsequent study with much greater power did not find evidence that GAD2 was involved with diabetes (5), and a small study showed no association with GAD2 antibody levels (6).

GAD2 is located on chromosome 10 (7) in a region that has been linked to obesity in family studies (8, 9, 10). Three polymorphisms in this gene have been associated with severe obesity in a large French cohort of 575 severely obese subjects, although the polymorphisms did not explain a large proportion of the strong linkage signal found in the family study (11). A case-control analysis in that study replicated the family-based association. One of the polymorphisms tested, A-243G, may have functional consequences on promoter expression (11) and on lower birth weight, lower insulinogenic index, and greater obesity in children (12). Another polymorphism, T83897A, was associated with insulin levels and secretion. These polymorphisms were also related to higher hunger and disinhibition scores (11). Using a large cohort of 855 severely obese subjects in Utah and two control groups (Table 1), the three polymorphisms in the GAD2 gene were tested for association to see whether these findings could be replicated.

Table 1.  Characteristics of the morbidly obese and normal-weight samples
VariableMorbidly obeseRandom normal weightVolunteer normal weight
  1. Means ± standard deviation or percentages are reported. Age was significantly lower and all other variables significantly higher in the morbidly obese group at p < 0.001 compared with each of the normal-weight groups. HOMA-IR, homeostasis model assessment of insulin resistance; HOMA-B, homeostasis model assessment of beta cell function.

Women (%)827466
Age (years)43.7 ± 11.451.7 ± 7.750.6 ± 9.7
BMI (kg/m2)48.3 ± 6.822.1 ± 1.822.4 ± 1.7
Glucose (mg/dL)103.1 ± 25.985.6 ± 9.383.5 ± 6.7
Insulin (μU/mL)18.1 ± 15.09.3 ± 5.8 
HOMA-IR4.6 ± 4.02.0 ± 1.4 
HOMA-B%216 ± 242165 ± 139 

Genotypes were first obtained for single nucleotide polymorphisms (SNPs) A-243G, C61450A, and T83897A in a series of 462 subjects who were randomly sampled from the Utah population. Mean age of the total random sample was 54 ± 7, and mean BMI was 28 ± 6 kg/m2. Allele frequencies of the A allele in the Utah population were estimated as 30.5% for C61450A, 19.3% for T83897A, and 81.2% for A-243G. After deleting the random subjects with a fasting glucose ≥ 126 mg/dL, there were no significant differences in the frequencies of the three genotypes between the normal-weight (BMI < 25 kg/m2; N = 130) and severely obese (BMI ≥ 35 kg/m2; N = 64) randomly ascertained subjects (p = 0.59, p = 0.33, and p = 0.49) or between the obese (BMI ≥ 30 kg/m2; N = 302) and non-obese (BMI < 30 kg/m2; N = 295) subjects (p = 0.69, p = 0.48, and p = 0.78) for SNPs A-243G, C61450A, and T83897A, respectively. There were too few (N = 20) severely obese subjects in the random group for comparison with the normal-weight group.

The genotype and allele frequency distributions of the subset of 130 normoglycemic, normal-weight subjects were compared with 855 severely obese subjects (BMI ≥ 40 kg/m2) examined before gastric bypass surgery (13). There were no significant differences for any of the three SNPs (Table 2). The associations were reexamined using logistic regression to control for age and sex differences between groups. None of the individual genotype or minor allele odds ratios (ORs) was significant for frequency differences between the severely obese and normal-weight groups for any SNP (Table 3). Adjustments of the p values for multiple comparisons were not made because this study was trying to replicate previous findings; however, multiple comparison adjustment of the p values would make all results even less significant. Additional logistic models were fit assuming that the G allele of A-243G was either dominant or recessive. Neither model [dominant OR = 1.30 (0.87, 1.93); recessive OR = 0.35 (0.08, 1.54)] showed significant associations of the SNP with severe obesity. Mean levels of glucose, insulin, homeostasis model assessment (HOMA)-insulin resistance (IR), and HOMA-beta cell function percentage (B%) in the normal-weight, normoglycemic controls did not differ among genotypes for any of the three SNPs (Table 4).

Table 2.  Comparison of single nucleotide polymorphism genotype and minor allele frequencies in 855 severely obese subjects with 130 normal-weight subjects
SNPCommon homozygotesHeterozygotesMinor allele homozygotesMinor allelep
  1. Common allele listed first in single nucleotide polymorphism name.

Table 3.  Logistic regression odds ratios for severe obesity, adjusted for age and sex, with the common allele homozygotes or the common allele as referent groups
SNPHeterozygotesMinor allele homozygotesMinor allele
  1. Common allele listed first. Odds ratios and 95% confidence intervals are presented for the genotype tests and the allele tests.

C61450A0.68 (0.45, 1.02)1.11 (0.52, 2.33)0.88 (0.66, 1.18)
T83897A0.72 (0.48, 1.08)1.66 (0.46, 5.97)0.87 (0.62, 1.22)
A-243G0.70 (0.47, 1.05)2.55 (0.58, 11.28)0.90 (0.64, 1.27)
Table 4.  Age- and sex-adjusted means ± standard error of the mean by single nucleotide polymorphism genotype in 130 normal-weight, normoglycemic controls
SNPCommon homozygotesHeterozygotesMinor allele homozygotesp
  1. HOMA-IR, homeostasis model assessment of insulin resistance; HOMA-B%, homeostasis model assessment of percentage of beta cell function.

Glucose (mg/dL)    
 C61450A86.6 ± 1.486.7 ± 1.285.3 ± 3.00.90
 T83897A86.8 ± 1.286.7 ± 1.481.4 ± 5.40.63
 A-243G87.0 ± 1.286.0 ± 1.485.5 ± 6.50.83
Insulin (μU/mL)    
 C61450A10.5 ± 0.98.7 ± 0.86.6 ± 1.80.08
 T83897A10.0 ± 0.78.2 ± 0.98.1 ± 3.40.24
 A-243G10.0 ± 0.78.0 ± 0.99.6 ± 4.10.18
 C61450A2.3 ± 0.21.9 ± 0.21.4 ± 0.50.11
 T83897A2.2 ± 0.21.8 ± 0.21.6 ± 0.80.33
 A-243G2.2 ± 0.21.7 ± 0.22.0 ± 1.00.25
 C61450A187.3 ± 21.1140.8 ± 18.3105.9 ± 44.20.10
 T83897A173.4 ± 18.1129.6 ± 20.8152.4 ± 81.10.25
 A-243G171.5 ± 18.1131.3 ± 20.8162.7 ± 98.20.32

Because the number of normal-weight controls was smaller than the number of severely obese cases and could have less precise frequency estimates and because the previously observed allelic associations were reversed in these data, we genotyped a volunteer sample of 134 healthy, normal-weight, normal-glucose subjects. There were no significant differences in frequencies between this volunteer group and the severely obese group. Combining the two control groups yielded ORs for the A-243G SNP of 0.73 (0.54, 1.00) and 0.98 (0.44, 2.18) for AG vs. AA and GG vs. AA, respectively.

Haplotypes were estimated from A-243G, C61450A, and T83897A for each subject and tested for differences between the severely obese and normal-weight subjects by logistic regression. There were three common haplotypes: ACT (68%), GAA (16%), and AAT (11%), with the remaining haplotypes being combined into a single haplotype (5%). Severely obese subjects had an ACT frequency of 68.0% vs. 66.5% for the normal-weight subjects compared with 65.3% and 71.2% in the French study, respectively. ORs for GAA (the three minor alleles) and AAT vs. ACT (the three major alleles) were 0.78 (0.55, 1.12) and 0.90 (0.59, 1.37), respectively, with the overall test for differences among the haplotypes being p = 0.10.

This study had over 95% power to detect the significant mean differences found in the French study for insulin and HOMA-B. Power to detect small differences in proportions is usually low and requires extremely large sample sizes. Therefore, neither the French study nor ours had 80% power to detect a difference in frequencies of only 4% (17.3% vs. 21.3% for A-243G). Our study had only 30% power to detect a significant effect at α = 0.05 and Nh = 407 (harmonic mean of 855 and 264), whereas the French study had ∼40% because their control group was larger (Nh = 592) (14). The allele frequencies for the minor allele of the three SNPs and comparisons with the other study groups in Utah and France are shown in Table 5. Our point estimates in the random controls were all in the opposite direction, and unless the estimates change with increasing sample size, they provide no evidence for replication. Table 3 suggested that the heterozygote risk for all three SNPs was not intermediate between the two homozygote risks, implying non-linearity even if the risks were significant. Consideration of dominant or recessive models did not improve the significance levels.

Table 5.  Comparison of minor allele frequencies* of GAD2 polymorphisms in Utah and French subjects
  • *

    Allele frequencies of A for 61450 and 83897 or G for −243. Allele frequencies from the French subjects estimated from the pooled set of subjects in Table 2 of Boutin et al. (11).

 Severely obese30.318.818.1
 Normal weight: random32.720.419.2
 Normal weight: volunteer28.420.521.6
 Severely obese32.319.621.3
 Normal weight28.617.417.3

A second test of the primary hypothesis was available using only the randomly ascertained subjects from the Utah population. The obese subjects in this series did not have significantly different allele frequencies from the non-obese random subjects, and the normal-weight subjects did not differ from the severely obese random subjects. Finally, in a second series of normal-weight subjects, despite its being a volunteer sample, fairly consistent allele frequency estimates with both the severely obese and random normal-weight subjects were seen. The allele frequency estimates for C61450A from the two control groups bracketed the estimates of the severely obese group, suggesting that larger sample sizes would not produce consistent differences between both control groups and the cases. Misclassification of the controls is unlikely because the random controls were 8 years older than the cases. It is rare for persons age 52 and normal weight to later become severely obese.

Despite having almost 50% more severely obese subjects than the French study, we were not able to confirm an association between GAD2 SNPs and severe obesity or IR or sensitivity. The study by Boutin et al (11) found association in their first series of severely obese subjects but could not confirm it in a second series, although combination of both sets retained the significance found in the first set. The normal variation of estimates among the various samples seen in these studies suggests a cautious interpretation of the reported association of the GAD2 gene with severe obesity (11) in all populations. However, the molecular, biochemical, and behavioral findings in the French subjects are consistent with a real effect in that population. Even for genes that have many positive associations with disease, replication is not always found. Reasons for lack of replication of the GAD2 gene between Utah and French subjects may include differences in diet and lifestyle. The prevalence of obesity in the U.S. is higher than in France, suggesting such population differences (15, 16). Future studies of association of these SNPs with biochemical pathways and abnormalities of intermediate phenotypes of obesity may more rigorously prove or disprove the suggested statistical association.

Research Methods and Procedures

Randomly ascertained subjects consisted of a sampling of unrelated individuals participating in our population-based Health Family Tree Program (17, 18). In brief, high school students in health classes throughout Utah collected health information on family members with the help of their parents. The data were computerized, and feedback was provided to students and their families regarding familial disease tendencies. The parents of the students were randomly selected by computer and invited to participate in our clinical studies. Subjects selected from Health Family Trees for other studies have been found to be representative of the Utah population (19, 20).

The severely obese subjects were participants in the Utah Obesity Study of the effectiveness of gastric bypass surgery (13). This study enrolled 1156 severely obese subjects (BMI ≥ 35 kg/m2), all of whom had a baseline clinic exam and blood draw. They were selected either because they sought gastric bypass surgery (N = 835) or because they were reported to be severely obese by participants in the Health Family Tree program (N = 321, non-overlapping with the random sample). None of these subjects had undergone previous surgery for weight loss. Approximately 93% of the subjects were white. Approximately 96% of severely obese subjects in the gastric bypass registry had strong family histories of obesity (two or more severely obese relatives). In fact, 75% reported five or more severely obese relatives, showing the strong familial aggregation of this trait. After analyzing these two groups of subjects, we genotyped a third group of 134 healthy, normal-weight, normal-glucose volunteer subjects to reinforce our results from the random sample of normal-weight subjects. All subjects signed an informed consent, and the study was approved by the University of Utah Institutional Review Board.

Height was measured using a Harpenden anthropometer (Holtain, Ltd., Crymych, United Kingdom) to the nearest centimeter. Weight was measured with a Scaletronix scale (model 5100; Scaletronix Corporation, Wheaton, IL). The scale has an 800-pound capacity and weighing accuracy of 0.1 kg. Blood was drawn in the sitting position after an overnight, 12-hour fast. Glucose and insulin were measured from these samples, and HOMA-IR, measuring IR, and HOMA-B%, measuring insulin secretion, were calculated using standard formulas (21). Glucose was converted from milligrams per deciliter to millimolar before use in the HOMA formulas. Insulin was measured in microunits per milliliter. DNA was extracted using QIAamp DNA Blood Kits (QIAGEN GmbH, Hilden, Germany). Primers and probes were designed to genotype the three SNPs for GAD2 previously studied in France (11), C61450A (rs992990), T83897A (rs928197), and A-243G (rs2236418), on a Roche LightTyper melting temperature machine (Roche Diagnostics, Indianapolis, IN). Genotypes from all three SNPs were in Hardy-Weinberg equilibrium in both cases and controls (p > 0.05). Linkage disequilibrium among markers was calculated using the correlation coefficient, r = D/(p1p2q1q2)1/2, where D = p11p22 − p12p21 (22). Linkage disequilibrium estimates for A-243G and C61450A, A-243G and T83897A, and T83897A and C61450A were 0.61, 0.81, and 0.70, respectively.

Comparisons of allele or genotype frequencies were made by a χ2 test. Means and standard deviations for each genotype were compared by analysis of covariance, with adjustment for age and sex. Logistic regression was used to estimate the odds of being in the obese group, for each of the three genotypes, adjusting for age and sex. Ninety-five percent confidence intervals are provided. Haplotypes of the three SNPs were estimated by PHASE 2.02 (23). Each haplotype was considered as an independent allele in the logistic regression model.


This study was supported by National Institute of Diabetes and Digestive and Kidney Diseases Grant DK055006 and by National Center for Research Resources Public Health Service Research Grant M01-RR00064.


  • 1

    Nonstandard abbreviations: GAD2, glutamate decarboxylase 2; SNP, single nucleotide polymorphism; OR, odds ratio; HOMA-IR, homeostasis model assessment of insulin resistance; HOMA-B, homeostasis model assessment of percentage of beta cell function.