Increased Burden of Rare Sequence Variants in GnRH-Associated Genes in Women With Hypothalamic Amenorrhea

J Clin Endocrinol Metab. 2021 Mar 8;106(3):e1441-e1452. doi: 10.1210/clinem/dgaa609.


Context: Functional hypothalamic amenorrhea (HA) is a common, acquired form of hypogonadotropic hypogonadism that occurs in the setting of energy deficits and/or stress. Variability in individual susceptibility to these stressors, HA heritability, and previous identification of several rare sequence variants (RSVs) in genes associated with the rare disorder, isolated hypogonadotropic hypogonadism (IHH), in individuals with HA suggest a possible genetic contribution to HA susceptibility.

Objective: We sought to determine whether the burden of RSVs in IHH-related genes is greater in women with HA than controls.

Design: We compared patients with HA to control women.

Setting: The study was conducted at secondary referral centers.

Patients and other participants: Women with HA (n = 106) and control women (ClinSeq study; n = 468).

Interventions: We performed exome sequencing in all patients and controls.

Main outcome measure(s): The frequency of RSVs in 53 IHH-associated genes was determined using rare variant burden and association tests.

Results: RSVs were overrepresented in women with HA compared with controls (P = .007). Seventy-eight heterozygous RSVs in 33 genes were identified in 58 women with HA (36.8% of alleles) compared to 255 RSVs in 41 genes among 200 control women (27.2%).

Conclusions: Women with HA are enriched for RSVs in genes that cause IHH, suggesting that variation in genes associated with gonadotropin-releasing hormone neuronal ontogeny and function may be a major determinant of individual susceptibility to developing HA in the face of diet, exercise, and/or stress.

Trial registration: NCT01500447 NCT00494169.

Keywords: GnRH deficiency; exome sequencing; female reproduction; genetics; hypogonadotropic hypogonadism.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Amenorrhea / epidemiology
  • Amenorrhea / etiology
  • Amenorrhea / genetics*
  • Case-Control Studies
  • Child
  • DNA Mutational Analysis
  • Exome Sequencing
  • Female
  • Gene Frequency
  • Genetic Association Studies
  • Genetic Predisposition to Disease
  • Gonadotropin-Releasing Hormone / metabolism*
  • Humans
  • Hypogonadism / epidemiology
  • Hypogonadism / etiology
  • Hypogonadism / genetics
  • Hypothalamic Diseases / complications
  • Hypothalamic Diseases / epidemiology
  • Hypothalamic Diseases / genetics*
  • Metabolic Networks and Pathways / genetics
  • Middle Aged
  • Mutation, Missense
  • Young Adult


  • Gonadotropin-Releasing Hormone

Associated data