Research Article

Discovery of a Novel Variant of SEMA3A in a Chinese Patient with Isolated Hypogonadotropic Hypogonadism

Table 1

Clinical data of the IHH proband carrying SEMA3A variant.

IDDxc.HGVSp.HGVSHormone levelsOther phenotypesSegregationMAFACMGIn silico prediction
LHFSHTEMatchedAllCADDSIFTPolyPhen2MutationTaster

1nIHHSEMA3A c.1369G > Ap.R457Q0.090.25119Pat00U25.5TPD
SEMA4G:c.1243C > Ap.R415SMat0.0090.0007U22.7TPD
PLXNA4:c.1262G > Ap.G421EMat0.0010.0001U23.6DPD
PLXND1:c.5671G > Ap.A1891TMat0.0040.0003U25.4TPD
FGFR1 c.400_401delinsGAp.S134DMat00LP22.8DPD

Normal adult men reference range for testosterone (T) 1.75–7.81 ng/mL, for estradiol (E2) < 53 pg/mL, for luteinizing hormone (LH) 1.2–8.6 mIU/mL, and for follicle-stimulating hormone (FSH) 1.3–19.3 mIU/mL. Dx, diagnosis; KS, Kallmann syndrome; nIHH, normosmic idiopathic hypogonadotropic hypogonadism; HGVS, Human Genome Variation Society; Mat, maternal. Pat, paternal. MAF, minor allele frequency in gnomAD database; Matched, ethnically matched population in gnomAD; All, all populations in gnomAD. ACMG criteria: P, pathogenic; B, benign; U, uncertain significance; LP, likely pathogenic; LB, likely benign. CADD, combined annotation-dependent depletion. CADD, SIFT, PolyPhen2, and MutationTaster (MutationT) were used for in silico prediction for the effect of the variants. SIFT: T, tolerated; D, deleterious. PolyPhen2: B, benign; P, possibly damaging; D, probably damaging. MutationTaster: N, polymorphism; D, disease causing.