| Literature DB >> 34636164 |
Meichao Men1,2, Dan-Na Chen3, Jia-Da Li4,5,6, Xinying Wang4,5,6, Wang Zeng4,5,6, Fang Jiang4,5,6, Ruizhi Zheng7, Wenting Dai1.
Abstract
BACKGROUND: Isolated hypogonadotropic hypogonadism (IHH) is a clinical syndrome described by failure of gonadal function secondary to defects on the synthesis, secretion, or action of the gonadotropin-releasing hormone (GnRH). The secreted glycoprotein SEMA3A binds its receptors NRP1 or NRP2 and PLXNA to participate in axonal projection, dendritic branching, synaptic formation, and neuronal migration. Deficiency in SEMA3A, NRP1, NRP2, and PLXNA1 have been related to abnormal GnRH neuron development in mice and IHH in humans.Entities:
Keywords: zzm321990NRP1zzm321990; zzm321990NRP2zzm321990; zzm321990PLXNA1zzm321990; idiopathic hypogonadotropic hypogonadism; whole exome sequencing
Mesh:
Substances:
Year: 2021 PMID: 34636164 PMCID: PMC8606218 DOI: 10.1002/mgg3.1816
Source DB: PubMed Journal: Mol Genet Genomic Med ISSN: 2324-9269 Impact factor: 2.183
FIGURE 1Schematic representation of the PLXNA1, NRP1, and NRP2 protein, showing the positions of the missense variants found in IHH patients. Abbreviations are as follows: sema, semaphorin domain; PSI, plexin/semaphorin/integrin domain; IPT, immunoglobulin‐like fold in plexins/transcription factors; TM, transmembrane domain; GAP1, Ras GTPase‐activating protein domain; RBD, Rho family GTPase‐binding domain. CUB, complement components C1r and C1s/uEGF/BMP‐1; CF5 and CF8, coagulation factors V and VIII; MAM, meprin/A5 antigen/receptor‐like protein tyrosine phosphatase μ
FIGURE 2The Family analysis of IHH probands with variants in PLXNA1, NRP1, and NRP2. Members of the family are showed by the Roman and Arabic numerals below the symbol, and the Roman numerals denote generations. Squares, male; circles, female; arrow, the proband
The prediction of PLXNA1, NRP1, and NRP2 variants using CADD, SIFT, Polyphen2, and MutaionTaster
| Nucleotide change | Protein change | Inheritance | ACMG | CADD Score | SIFT | Polyphen2 | MutaionTaster |
|---|---|---|---|---|---|---|---|
| PLXNA1 c.119C>G | p.P40R | N/A | LB | 0.002 | T | B | N |
| PLXNA1 c.G1471A | p.V491I | N/A | U | 22.8 | T | B | D |
| PLXNA1 c.2519G>A | p.R840Q | N/A | U | 26.3 | T | D | D |
| PLXNA1 c.C2543G | p.P848R | N/A | U | 8.455 | T | B | N |
| PLXNA1 c.C3200T | p.T1067M | N/A | U | 28.8 | D | D | D |
| PLXNA1 c.C3317T | p.A1106V | Maternal | U | 24.5 | D | B | D |
| PLXNA1 c.G3337C | p.V1113L | N/A | LB | 0.351 | T | B | N |
| PLXNA1 c.G3401A | p.R1134H | N/A | U | 22.9 | D | B | N |
| PLXNA1 c.C3629T | p.A1210V | N/A | U | 23.5 | D | B | D |
| PLXNA1 c.C5126T | p.S1709L | N/A | U | 25.1 | D | P | D |
| NRP1: c.A418C | p.I140L | N/A | U | — | D | B | D |
| NRP1: c.676C>T | p.R226C | Maternal | U | 35 | D | D | D |
| NRP1: c.A1274T | p.K425M | Maternal | U | — | D | D | D |
| NRP1 c.C1571T | p.S524L | N/A | U | — | D | P | D |
| NRP1 c.C1676T | p.T559M | N/A | U | 25.6 | T | D | D |
| NRP1 c.2200G>A | p.G734S | N/A | U | — | T | P | D |
| NRP1 c.2596G>A | p.A866T | N/A | U | — | D | P | D |
| NRP1 c.T2633C | p.V878A | N/A | U | 25.6 | D | D | D |
| NRP2 c.2033G>A | p.R678Q | Maternal | LB | 8.318 | T | B | N |
| NRP2 c.C2773A | p.Q925K | N/A | U | — | D | D | D |
ACMG criteria: P, pathogenic; B, benign; U, uncertain significance; LP, likely pathogenic; LB, likely benign. CADD, combined annotation dependent depletion; A scaled CADD score of 20 means that a variant is among the top 1% of deleterious variants in the human genome; a scaled CADD score of 30 means that the variant is in the top 0.1%. SIFT: T, tolerated; D, deleterious. PolyPhen‐2: B, benign; P, possibly damaging; D, probably damaging. Mutation Taster: P, Polymorphism automatic; N, polymorphism; D, disease causing; NA, not available.
Clinical information of IHH patients with PLXNA1, NRP1, and NRP2 variants
| ID | Age | Sex | Dx | Nucleotide change | Protein change | Hormone levels | Other phenotypes | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LH | FSH | T | E2 | |||||||
| 1 | 27 | M | KS | PLXNA1 c.119C>G | p.P40R | 0.48 | 3.66 | 3.17 | 13.07 | Cryptorchidism |
| OTUD4 c.A611G | p.Q204R | |||||||||
| 2 | — | M | KS | PLXNA1 c.G1471A | p.V491I | 0.3 | 1.0 | 0.5 | 12 | — |
| 3 | 27 | M | KS | PLXNA1 c.2519G>A | p.R840Q | 0.07 | 0.45 | 0.25 | <10 | Impaired hearing |
| SOX10 c.G122T | p.G41V | |||||||||
| 4 | 26 | M | nIHH | PLXNA1 c.C2543G | p.P848R | 0.01 | 1.2 | 0.1 | 19 | — |
| NRP2 c.C2773A | p.Q925K | |||||||||
| 5 | 16 | F | nIHH | PLXNA1 c.C3200T | p.T1067M | 0.04 | 0.3 | 0.41 | 20.81 | Impaired hearing |
| CHD7 c.G3143A | p.G1048E | |||||||||
| CHD7 c.A3145T | p.S1049C | |||||||||
| 6 | 11 | M | KS | PLXNA1 c.C3317T | p.A1106V | 0.4 | 4.61 | <0.01 | <0.01 | — |
| NR0B1 c.C875A | p.A292E | |||||||||
| 7 | 19 | M | KS | PLXNA1 c.G3337C | p.V1113L | 0.4 | 1.0 | 0.5 | 29 | — |
| 8 | 15 | M | nIHH | PLXNA1 c.G3401A | p.R1134H | 0.1 | 0 | 0.5 | 21 | Azoospermia in testis, |
| SEMA3E c.196T>C | p.Y66H | High myopia | ||||||||
| 9 | 26 | M | KS | PLXNA1 c.G3401A | p.R1134H | 0.91 | 1.05 | 0.37 | 5.71 | — |
| 10 | 21 | F | KS | PLXNA1 c.C3629T | p.A1210V | 0.6 | 2.3 | <20 | 39.5 | Right renal agenesis |
| SPRY4 c.A202T | p.T68S | |||||||||
| 11 | 25 | M | nIHH | PLXNA1 c.C5126T | p.S1709L | 0.2 | 1.1 | 0.9 | 22 | Azoospermia in testis, cubitus valgus |
| 12 | — | F | KS | NRP1: c.A418C | p.I140L | 0.1 | 2.2 | 0.4 | 20 | Impaired hearing |
| 13 | — | M | KS | NRP1: c.676C>T | p.R226C | 0.22 | 4.2 | 0.3 | 18 | Impaired hearing |
| PROK2: c.153G>C | p.W51C | |||||||||
| 14 | — | M | KS | NRP1: c.A1274T | p.K425M | 0.19 | 2.1 | 0.5 | 19 | — |
| 0 | PROKR2: c.G533C | p.W178S | ||||||||
| 15 | — | M | KS | NRP1 c.C1571T | p.S524L | 0.06 | 0.4 | 0.22 | 15 | — |
| FGFR1 c.1019C>T | p.T340M | |||||||||
| PROKR2 c.G1058A | p.R353H | |||||||||
| 16 | — | M | KS | NRP1 c.C1676T | p.T559M | 0.3 | 1.6 | 0.7 | 28 | — |
| PROKR2 c.G533C | p.W178S | |||||||||
| 17 | 47 | M | KS | NRP1 c.2200G>A | p.G734S | 0.91 | 2.05 | 0.32 | 37.45 | — |
| PNPLA6 c.1159C>A | p.P387T | |||||||||
| 18 | 25 | M | KS | NRP1 c.2596G>A | p.A866T | 0.13 | 0.83 | 0.2 | 10 | Cubitus valgus, right cryptorchidism |
| PNPLA6 c.3371G>A | p.C1124Y | |||||||||
| CCDC141 c.4152G>C | p.R1384S | |||||||||
| 19 | 11 | F | KS | NRP1 c.T2582C | p.V878A | 0 | 0.4 | 15.4 | 0.16 | — |
| IL17RD c.C572T | p.P191L | |||||||||
| PROKR2 c.G533C | p.W178S | |||||||||
| 20 | 19 | F | nIHH | NRP2 c.2033G>A | p.R678Q | 0.09 | 0.5 | 0.25 | 23.68 | — |
| GNRHR c.719G>A | p.R240Q | |||||||||
The normal ranges were as follows: FSH, 1.3–19.3 UI/L; LH, 1.2–8.6 UI/L; E2, >20 pg/mL; t, 1.75–7.81 ng/mL.
Abbreviations: Dx, diagnosis; E2, estradiol; F, female; FSH, follicle stimulating hormone; KS, Kallmann syndrome; LH, luteinizing hormone; M, male; nIHH, normosmic isolated hypogonadotropic hypogonadism;T, testosterone.