1. NGS panel - Genetic testing for Kallmann syndrome and hypogonadotropic hypogonadism

Kallmann syndrome and hypogonadotropic hypogonadism

August 22, 2017

Inheritance pattern

Autosomal recessive, autosomal dominant, X-linked

Clinical features

Kallmann syndrome (KS) is a developmental genetic disorder characterized by delayed or absent puberty and impaired sense of smell and it belongs to isolated gonadotropin-releasing hormone deficiencies. Deficient hypothalamic gonadotropin-releasing hormone (GnRH) secretion underlies the markedly abnormal gonadotropin secretion patterns in most patients with Kallmann syndrome or idiopathic hypogonadotropic hypogonadism. The result is hypogonadism; infertility; and absent, incomplete, or partial pubertal maturation.

Incidence of Kallmann syndrome was estimated to be 1:30,000 in males and 1:125,000 in females in Finland with the male-to-female ratio of nearly 4:1 1.

Patients with classic Kallmann syndrome or idiopathic hypogonadotropic hypogonadism may not experience puberty or may experience incomplete puberty and have symptoms associated with hypogonadism. For men, these symptoms include decreased libido, erectile dysfunction, decreased muscle strength, and diminished aggressiveness and drive 2, 3. For women, symptoms include amenorrhea and dyspareunia. Family members of patients with idiopathic hypogonadotropic hypogonadism may have a history of delayed, although otherwise normal, puberty 2, 3.

The impaired olfactory function in Kallmann syndrome can be either hyposmia or complete anosmia 2, 3. Most individuals with impaired sense of smell are otherwise asymptomatic. Isolated gonadotropine deficiency is associated with a normal sense of smell (“normosmic”) in approximately 40% of affected individuals and with an impaired sense of smell (Kallmann syndrome) in approximately 60% of affected cases 2, 3.

Laboratory findings of Kallmann syndrome and hypogonadotropic hypogonadism include reduced levels of testosterone in males and estradiol in females, as well as very low serum concentrations of LH (luteinizing hormone) and FSH (follicle stimulating hormone). Levels of other anterior pituitary hormones are typically normal.

Table 1. Overview of genes associated with Kallmann syndrome and hypogonadotropic hypogonadism

Gene OMIM (Gene) Associated diseases (OMIM) Inheritance CentoMD® exclusive variant numbers (++)
ANOS1 300836 Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1) XL R 9
CHD7 608892 CHARGE syndrome; Hypogonadotropic hypogonadism 5 with or without anosmia AD 89
DUSP6 602748 Hypogonadotropic hypogonadism 19 with or without anosmia AD 0
FEZF1 613301 Hypogonadotropic hypogonadism 22, with or without anosmia AR 0
FGF17 603725 Hypogonadotropic hypogonadism 20 with or without anosmia AD 0
FGF8 600483 Hypogonadotropic hypogonadism 6 with or without anosmia AD 11
FGFR1 136350 Pfeiffer syndrome; Jackson-Weiss syndrome; Hypogonadotropic hypogonadism 2 with or without anosmia; Osteoglophonic dysplasia; Trigonocephaly 1; Encephalocraniocutaneous lipomatosis; Hartsfield syndrome AD, Somatic mosaicism 22
FLRT3 604808 Hypogonadotropic hypogonadism 21 with anosmia AD 0
FSHB 136530 Hypogonadotropic hypogonadism 24 without anosmia AR 0
GNRH1 152760 ?Hypogonadotropic hypogonadism 12 with or without anosmia AR 5
GNRHR 138850 Hypogonadotropic hypogonadism 7 without anosmia AR 5
HESX1 601802 Growth hormone deficiency with pituitary anomalies; Pituitary hormone deficiency, combined, 5; Septooptic dysplasia AD, AR 0
HS6ST1 604846 Hypogonadotropic hypogonadism 15 with or without anosmia AD 2
IL17RD 606807 Hypogonadotropic hypogonadism 18 with or without anosmia AD, AR 2
KISS1 603286 ?Hypogonadotropic hypogonadism 13 with or without anosmia AR 4
KISS1R 604161 ?Precocious puberty, central, 1; Hypogonadotropic hypogonadism 8 with or without anosmia AD, AR 6
LHB 152780 Hypogonadotropic hypogonadism 23 with or without anosmia AR 0
NSMF 608137 Hypogonadotropic hypogonadism 9 with or without anosmia AD 1
PROK2 607002 Hypogonadotropic hypogonadism 4 with or without anosmia AD 3
PROKR2 607123 Hypogonadotropic hypogonadism 3 with or without anosmia AD 9
SEMA3A 603961 Hypogonadotropic hypogonadism 16 with or without anosmia AD 36
SPRY4 607984 Hypogonadotropic hypogonadism 17 with or without anosmia AD 0
TAC3 162330 Hypogonadotropic hypogonadism 10 with or without anosmia AR 0
TACR3 162332 Hypogonadotropic hypogonadism 11 with or without anosmia AR 4
WDR11 606417 Hypogonadotropic hypogonadism 14 with or without anosmia AD 12

A major treatment for Kallmann syndrome is hormone replacement therapy, based on the use of testosterone in males and estradiol in females. In addition, human chorionic gonadotropin (hCG) injections in males or progestin in females can be used in order to stimulate spermatogenesis or folliculogenesis. If conception fails despite spermatogenesis in a male or ovulation induction in a female, in vitro fertilization may be an option.

CENTOGENE offers sequencing and deletion/duplication analysis for the Kallmann syndrome and Hypogonadotropic hypogonadism panel (genes: ANOS1, CHD7, DUSP6, FEZF1, FGF17, FGF8, FGFR1, FLRT3, FSHB, GNRH1, GNRHR, HESX1, HS6ST1, IL17RD, KISS1, KISS1R, LHB, NSMF, PROK2, PROKR2, SEMA3A, SPRY4, TAC3, TACR3, WDR11). We also offer single gene tests for each gene included in the panel.

Differential diagnosis

The differential diagnosis of Kallmann syndrome related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Amenorrhea
  • Borjeson-Forssman-Lehmann syndrome
  • CHARGE syndrome
  • Constitutional growth delay
  • Erectile dysfunction
  • Follicle-stimulating hormone abnormalities
  • Infertility
  • Klinefelter syndrome
  • LEOPARD syndrome
  • Laurence-Moon-Biedl syndrome
  • Luteinizing hormone deficiency
  • Luteinizing hormone–releasing hormone deficiency
  • Martsolf syndrome
  • Prader-Willi syndrome
  • Rothmund-Thomson syndrome
  • Turner syndrome
  • Septooptic dysplasia.

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for Kallmann syndrome using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire gene (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Kallmann syndrome panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Kallmann syndrome panel, we further recommend continuing the bioinformatics analysis of the data with whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.

Referral reasons

The following individuals are candidates for Kallmann syndrome gene testing:

  • Individuals with a family history of Kallmann syndrome and presentation of the most common symptoms
  • Individuals without a positive family history, but with symptoms resembling Kallmann syndrome
  • Individuals with a negative but suspected family history, in order to perform proper genetic counseling (prenatal analyses are recommended in families with affected individuals).

Test utility

Sequencing, deletion/duplication of Kallmann syndrome related genes should be performed in all individuals suspected of having this particular phenotype. In parallel, other genes reported to be related with Kallmann syndrome should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of Kallmann syndrome, identify at-risk family members, provide reproductive risks as well as preconception/prenatal options, and allow for appropriate referral for patient support and/or resources.

More information on CENTOGENE´s Kallmann syndrome and hypogonadotropic hypogonadism panel can be found in our genetic test catalogue.