Non-Coding Structural Variants in Regulatory Regions and High Polygenic Burden May Jointly Contribute to Early-Onset Familial Hashimoto’s Thyroiditis

Background/Objectives: Multigenerational families with unusually early disease onset provide a unique opportunity to investigate the genetic architecture underlying the missing heritability of complex diseases. Here, we investigated the genetic basis of apparent autosomal dominant early-onset Hashimoto’s thyroiditis (HT) in a multigenerational pedigree using whole-exome sequencing (WES) in 9 individuals and PacBio HiFi long-read whole-genome sequencing (LR-WGS) in four family members spanning three generations. Methods: WES identified a rare disease-segregating TPH2 missense variant, while LR-WGS identified approximately 2000 structural variants (SVs) shared by the three sequenced affected relatives and absent from the unaffected father. Results: Affected-lineage-shared SVs were significantly enriched within established hypothyroidism GWAS loci (447 observed vs. 292.6 expected overlaps; p = 6.99 × 10−4), with prominent clusters at the NFATC1-ATP9B and PDCD6-AHRR loci. Integrative analyses incorporating regulatory annotation, GWAS overlap, and exploratory proteomic profiling highlighted candidate regulatory SVs affecting enhancers and long non-coding RNAs within the TPH2/TRHDE, TPO/LALTOP, and TSHR loci. Exploratory proteomic profiling was consistent with involvement of the NFATC1-ATP9B and PDCD6-AHRR loci and identified AXIN1 as an additional candidate locus. Parallel polygenic risk score (PRS) analysis showed that the three affected sequenced family members ranked above the 95th percentile of the HT PRS distribution. Conclusions: Together, these findings are consistent with a multi-hit genetic model in which elevated polygenic burden and multiple regulatory structural variants may jointly contribute to early-onset familial HT. The observed enrichment of affected-lineage-shared SVs within established hypothyroidism GWAS loci further suggests that regulatory structural variation may contribute to previously unexplained non-coding genetic susceptibility.