Table 5.

Rare variants: SNP carriage frequencies of homozygous plus heterozygous variants vs wild type variants

Gene and Corrected P-values
SS Disease	Growth Pathway	Adult Height
NPR2 (↓) p = 7.22E-04	BUB1B (↓) p = 1.59E-07	PTCH1 (↓) p = 7.22E-04
TRIP11 (↓) p = 1.55E-03	ELK1 (↓) p = 5.18E-03	NHEJ1 (↓) p = 4.85E-03
FANCM (↓) p = 1.18E-02	DGKE (↑) p = 9.01E-03	TEAD3 (↑) p = 7.08E-03
CUL7 (↓) p = 1.60E-02	IGFBPI (↓) p = 4.63E-02	NFKB1 (↓) p = 1.03E-02
FANCA (↓) p = 5.04E-02	PEX2 (↓) p = 4.63E-02	SH2B1 (↑) p = 1.03E-02
		LEPRE1 (↓) p = 2.95E-02
		MC4R (↓) p = 5.04E-02
		BCAS3 (↓) p = 5.04E-02
		DLEU7 (↓) p = 5.04E-02

For those variants with a minor allele frequency of < 2%, SNP/indel frequency was assessed for carriage of homozygous plus heterozygous variants versus wild type. Nineteen genes were identified where SNP carriage frequencies were significantly different, with a Benjamini-Hochberg-corrected P-value of ≤ 0.05. In SS-UA, SNP frequencies were increased in 3 genes and decreased in 16. These included genes that are associated with SS conditions, genes associated with growth pathways, and genes associated with adult height. The most significant genes in each of these groups were NPR2, BUB1BI, and PTCH1.