Identification of Novel Genetic Variants in a Cohort of Congenital Hypogonadotropic Hypogonadism: Computational Analysis of Pathogenicity Predictions
Abstract
1. Introduction
2. Results
2.1. Clinical Features of the HH Cohort
2.2. Genetic Variants and Their Pathogenicity
2.3. Oligogenic Transmission in Three Patients with CHH
2.4. Frequency of Variants According to Phenotype
2.5. Functional Characterization of ANOS1 and IL17RD Mutations
2.6. Molecular Dynamics Simulations of WDR11 Variant
3. Discussion
4. Materials and Methods
- -
- low serum testosterone concentrations in the setting of low gonadotropin concentrations (<264 ng/dL in adults);
- -
- delayed/absent pubertal development, defined by lack of testicular enlargement (volume < 4 mL with Prader orchidometer) in boys at age 14 and absence of breast development in girls at age 13; and/or
- -
- infertility/sterility; and/or
- -
- criptorchidism and micropenis in the neonatal period; and/or
- -
- anosmia/hyposmia assessed by Sniffin’ test (Sense Trading BV, Groningen, The Netherlands), a validated measure of olfactory function; and/or
- -
- developmental anomalies, such as cleft lip and palate, dental agenesis, renal agenesis, hypospadias, bimanual synkinesis, sensorineural deafness, and skeletal anomalies; and/or
- -
- no identifiable cause of hypothalamic or pituitary dysfunction, such as chronic diseases, pituitary tumors, head trauma; and/or
- -
- presence of family cases of CHH and/or infertility sine causa.
4.1. Instrumental and Molecular Analyses
- i.
- Expression of the variant in a biological sample.
- ii.
- Investigation of the variant through MDs and dynamic cross-correlation analysis.
4.2. Reverse Transcription and Quantitative Real-Time Amplification (qRT-PCR)
4.3. Molecular Dynamics Simulations and Dynamic Cross-Correlation Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Pt 1 | Pt 2 | Pt 3 | Pt 4 | Pt 5 | Pt 6 | Pt 7 | Pt 8 | Pt 9 | Pt 10 | Pt 11 | Pt 12 | Pt 13 | Pt 14 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Age at diagnosis | 52 years | 18 years | 22 years | 18 years | 42 years | 7 months | 18 years | 17 years | 24 years | 16 years | 18 years | 30 years | 17 years | 17 years |
Sex | M | M | F | M | F | M | M | M | M | F | M | F | M | M |
Phenotype | KS | nHH | nHH | KS | KS | KS | nHH | KS | nHH | KS | KS | nHH | nHH | nHH |
Clinical characteristics | Hypogonadism Anosmia | Hypogonadism | Hypogonadism Secondary amenorrhea Ataxia | Hypogonadism Anosmia Eunuchoidal proportions | Hypogonadism Primary amenorrhea Anosmia | Cryptorchidism Micropenis Hypogonadism Anosmia | Hypogonadism | Hypogonadism Anosmia Eunuchoidal proportions | Hypogonadism Osteoporosis | Hypogonadism Primary amenorrhea Iposmia | Hypogonadism Gynecomastia Anosmia Eunuchoidal proportions | Hypogonadism Secondary amenorrhea | Cryptorchidism Hypogonadism Eunuchoidal proportions | Hypogonadism Eunuchoidal proportions |
Puberty | Absent | Absent | Normal | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Normal | Arrest | Absent |
CHH reversal | No | No | No | No | No | No | No | No | Yes | No | No | No | No | No |
Gene | ANOS1 | IL17RD | WDR11 DCC | PROK2 | FGF8 IL17RD | - | IL17RD | PROK2 | DCC | CHD7 TACR3 | FGFR11 | TACR3 | - | DUSP6 |
LH (IU/L) | 0.05 | 0.16 | 0.80 | 0 | 0.10 | 0.20 | 0.38 | 0.39 | 0.39 | 0.40 | 0.18 | 0.25 | 1.58 | 0.30 |
FSH (IU/L) | 1.48 | 3.05 | 0.90 | 0.68 | 0.34 | 0.70 | 1.56 | 0.54 | 0.54 | 2.15 | 1.30 | 0.90 | 1.89 | 1.05 |
Testosterone (ng/mL) or estradiol (pg/mL) | 113 | 20 | 10 | 0.30 | 10 | 0.03 | 0.18 | 14 | 14 | 11.80 | 14 | 15.2 | 19 | 12 |
Inhibin B (pg/mL) | 156 | 210 | 175 | 165 | 182 | 200 | 180 | 156 | 223 | 210 | ||||
AMH (ng/mL) | 3 | 1.2 | 4.2 | 2.6 | ||||||||||
Testicular volume (cm3) or ovarian volume (cm3) | 3.0 | 2.0 | 5.0 | 2.0 | 2.0 | 1.0 | <2.0 | 2.0 | 4.0 | <2.0 | 2.0 | 2.5 | 6.0 | 2.0 |
Brain MRI | Normal | Normal | Cerebellar atrophy | Normal | Hypoplasia of olfactory bulbs | Normal | Normal | Normal | Normal | Hypoplasia of olfactory bulbs | Normal | Normal | Normal | Normal |
Therapy | Testosterone/Gonadotropin | Gonadotropin/Testosterone | Estrogen/Gonadotropin/EP | Gonadotropin/Testosterone | Estrogen/Gonadotropin/EP | Gonadotropin/Testosterone | Testosterone/Gonadotropin | Gonadotropin | Testosterone | Estrogen | Gonadotropin/Testosterone | EP | Gonadotropin | Testosterone |
Gene | RefSeq/Variant Identified | Location | Consequence | Impact | Genotype | Inheritance | Clinical Significance |
---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4: c.541+1G>A GRCh37: ChrX:g.8565074C>T | Intron 4 | - | LOF | Hemizygous | AD | Probably pathogenic |
IL17RD | NM_017563.5: c.1303_1304dup GRCh37: Ch3:g.57132427_5713 | Exon 12 | (p.Lys436ThrfsTer58) | Frameshift LOF | Heterozygous | AR/AD/Oligo | Probably pathogenic |
DCC | NM_005215.4 c.3533C>T GRCh37: Chr18:g.50985742C>T | Exon 24 | (p.Ser1178Phe) | Missense | Heterozygous | AR/AD/Oligo | VUS |
WDR11 | NM_018117.12 c.2306T>G GRCh37 | Exon 18 | (p.Met769Arg) | Missense | Heterozygous | AD | VUS |
PROK2 | NM_001126128.2 c.146G>T | Exon 2 | (p.Ser49Ile) | Missense | Heterozygous | AR/AD/Oligo | VUS |
FGF8 | NM_033163.5 Chr1o: g.103530393C>T GFCh37 | Intron 5 | - | Missense | Heterozygous | AD/Oligo | VUS |
IL17RD | NM_017563.5 Chr3: c.1622C>T | Exon 12 | (p.Ser541Phe) | Missense | Heterozygous | AR/AD/Oligo | VUS |
IL17RD | NM_017563.5 c.692A>G | Exon 7 | (p.Tyr231CYS) | Missense | Heterozygous | AR/AD/Oligo | VUS |
PROK2 | NM_001126128.2 c.121G>A | Exon 2 | (p.Gly41Ser) | Missense | Heterozygous | AR/AD/Oligo | VUS |
DCC | NM_005215.4 c.1435A>G | Exon 9 | (p.Thr479Ala) | Missense | Heterozygous | AR/AD/Oligo | VUS |
CHD7 | NM_017780.4 | (p.Met340Val) | Missense | Heterozygous | AR | Benign | |
TACR3 | NM_001059 | (p.Lys286Arg) | Missense | Heterozygous | Benign | ||
FGFR11 | NM_023110.3 c.1058C>G | Exon 8 | (p.S353C) | Missense | Heterozygous | AR/AD/Oligo | VUS |
TACR3 | NM_001059.3 Chr4: c.101A>T | Exon 4 | (p.Lys361Ter) | LOF | Heterozygous | AR | Probably pathogenic |
TACR3 | NM_001959.3 Chr4: c.824G>A | Exon 3 | (p.Trp275Ter) | LOF | Heterozygous | AR | Pathogenic |
DUSP6 | NM_001946.4 c.838+3G>C Chr12:g.89744362C>G hg19/GRCh37 | Intron 2 | - | Missense | Heterozygous | AR | VUS |
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Chiarello, P.; Gualtieri, G.; Bossio, S.; Seminara, G.; Molinaro, M.; Antonucci, G.; Perri, A.; Rocca, V.; Cannarella, R.; La Vignera, S.; et al. Identification of Novel Genetic Variants in a Cohort of Congenital Hypogonadotropic Hypogonadism: Computational Analysis of Pathogenicity Predictions. Int. J. Mol. Sci. 2025, 26, 5207. https://doi.org/10.3390/ijms26115207
Chiarello P, Gualtieri G, Bossio S, Seminara G, Molinaro M, Antonucci G, Perri A, Rocca V, Cannarella R, La Vignera S, et al. Identification of Novel Genetic Variants in a Cohort of Congenital Hypogonadotropic Hypogonadism: Computational Analysis of Pathogenicity Predictions. International Journal of Molecular Sciences. 2025; 26(11):5207. https://doi.org/10.3390/ijms26115207
Chicago/Turabian StyleChiarello, Paola, Gianmarco Gualtieri, Sabrina Bossio, Giuseppe Seminara, Marianna Molinaro, Gemma Antonucci, Anna Perri, Valentina Rocca, Rossella Cannarella, Sandro La Vignera, and et al. 2025. "Identification of Novel Genetic Variants in a Cohort of Congenital Hypogonadotropic Hypogonadism: Computational Analysis of Pathogenicity Predictions" International Journal of Molecular Sciences 26, no. 11: 5207. https://doi.org/10.3390/ijms26115207
APA StyleChiarello, P., Gualtieri, G., Bossio, S., Seminara, G., Molinaro, M., Antonucci, G., Perri, A., Rocca, V., Cannarella, R., La Vignera, S., Calogero, A. E., Greco, E. A., Iuliano, R., Alcaro, S., & Aversa, A. (2025). Identification of Novel Genetic Variants in a Cohort of Congenital Hypogonadotropic Hypogonadism: Computational Analysis of Pathogenicity Predictions. International Journal of Molecular Sciences, 26(11), 5207. https://doi.org/10.3390/ijms26115207