Table 2.
Prioritized heterozygous missense, truncating, and regulatory PAM variants that were functionally analyzed.
| DNA change | Protein change | SNP ID | Location in gene | Location in protein | MAF in our cohort (%) | Global control MAF (%) | Highest control population MAF (%) | # of homozygotes in gnomAD | P-value | In silico prediction | Individuals harboring the variant |
|---|---|---|---|---|---|---|---|---|---|---|---|
| c.-607A>G † | n.a. | rs76396377 | promoter | n.a. | 0.4 | 1.479 | 2.943 (African) | 24 | n.s. | 1 TF replaced | 1 from 1 FIPA (PRL) |
| c.-550G>T ‡ | n.a. | rs1007572715 | promoter | n.a. | 0.4 | 0.0072 | 0.0415 (South Asian) | 0 | <0.05 | 2 TFs lost | 1 acro |
| c.-361G>A | n.a. | rs143617515 | 5’UTR (exon 1) | n.a. | 1.21 | 0.6275 | 3.647 (Finnish) | 12 | n.s. | 2 TFs lost, 4 TFs created | 2 gigantism, 1 NFPA |
| c.-133T>C ¥ | n.a. | rs1413721196 | 5’UTR (exon 1) | n.a. | 0.25 | 0.0007 | 0.0015 (European) | 0 | <0.05 | 1 TF lost | 1 pediatric CD |
| c.-109G>C | n.a. | Novel | 5’UTR (exon 1) | n.a. | 0.25 | n.a. | n.a. | n.a. | n.a. | 1 TF replaced | 1 acro |
| c.-35C>G | n.a. | rs201016377 | 5’UTR (exon 1) | n.a. | 0.15 | 0.0749 | 0.9040 (Finnish) | 1 (Finnish) | n.s. | n.a. | 1 gigantism |
| c.79G>A ** | p.Val27Ile | rs199856250 | exon 1 | proregion | 0.16 | 0.0004 | 0.0008 (European) | 0 | <0.05 | VUS (1, 6, 12) | 1 acro |
| c.92T>A | p.Phe31Tyr | rs114014768 | exon 2 | linker region | 0.63 | 0.8654 | 2.814 (African) | 19 | n.s. | likely benign (0, 1, 16) | 2 acro, 1 gigantism, 1 pediatric CD |
| c.145G>C | p.Val49Leu | rs2230458 | exon 2 | PHMcc | 0.94 | 0.9278 | 1.803 (Finnish) | 5 (European) | n.s. | likely benign (0, 2, 17) | 2 gigantism, 3 pediatric CD, 1 PRL |
| c.239G>A | p.Arg80Gln | rs753307443 | exon 3 | PHMcc | 0.16 | 0.0026 | 0.0066 (Latino) | 0 | <0.05 | likely benign (1, 5, 13) | 1 from 1 FIPA (GH excess) |
| c.718C>T †† | p.His240Tyr | rs761898981 | exon 9 | PHMcc | 0.15 | 0.0039 | 0.0478 (Other) | 0 | <0.05 | VUS (0, 11, 7) | 1 gigantism |
| c.731T>C ¥¥ | p.Val244Ala | rs201009674 | exon 10 | PHMcc | 0.16 | 0.0533 | 0.6632 (Ashkenazi Jewish) | 0 | n.s. | likely pathogenic (6, 12, 0) | 1 pediatric CD |
| c.1235C>T ** | p.Pro412Leu | rs761619241 | exon 14 | linker region | 0.16 | 0.0016 | 0.0029 (Latino) | 0 | <0.05 | likely pathogenic (6, 9, 4) | 2 from 1 FIPA (heterogeneous) |
| c.1354A>G | p.Ile452Val | rs145710876 | exon 14 | linker region | 0.16 | 0.0151 | 0.0555 (African) | 0 | n.s. | likely benign (0, 0, 18) | 1 gigantism |
| c.1473A>C | p.Glu491Asp | rs61736661 | exon 14 | linker region | 0.16 | 0.6662 | 1.241 (European) | 8 (European) | n.s. | likely benign (0, 1, 16) | 1 from 1 FIPA (PRL) |
| c.1616C>G | p.Ser539Trp | rs78408340 | exon 16 | PALcc | 0.15 | 0.4169 | 0.7250 (European) | 2 (European) | n.s. | likely pathogenic (10, 6, 2) | 1 acro |
| c.1654G>A ‡‡ | p.Gly552Arg | rs201249509 | exon 16 | PALcc | 0.15 | 0.0053 | 0.0103 (European) | 0 | <0.05 | likely pathogenic (10, 6, 2) | 1 acro |
| c.1688A>G | p.Asp563Gly | rs35658696 | exon 16 | PALcc | 4.00 | 3.109 | 5.657 (European) | 108 | n.s. | likely pathogenic (4, 11, 1) | 13 acro, 5 gigantism, 4 PRL, 4 CD (3 pediatric, 1 silent) |
| c.1921G>C | p.Gly641Arg | rs775364358 | exon 18 | PALcc | 0.15 | 0.0033 | 0.0197 (Latino) | 0 | <0.05 | likely benign (0, 3, 16) | 1 PRL |
| c.2108G>A | p.Arg703Gln | rs761130902 | exon 19 | PALcc | 0.15 | 0.0013 | 0.0193 (East Asian) | 0 | <0.05 | likely pathogenic (10, 9, 0) | 4 (3 affected) from 1 FIPA (gigantism) |
| c.2276T>C †† | p.Phe759Ser | rs375364507 | exon 20 | PALcc | 0.15 | 0.0092 | 0.0206 (European) | 0 | n.s. | likely pathogenic (7, 11, 0) | 1 gigantism |
| c.2332-2A>T § | p.His778fs | rs1006675725 | intron 20 | PALcc | 0.15 | 0.0007 | 0.0015 (European) | 0 | <0.05 | pathogenic (disrupts canonical SA) | 2 (1 pediatric CD and unaffected mother) |
| c.*1455C>T ¥¥¥ | n.a. | rs146343559 | 3’UTR (exon 25) | n.a. | 0.67 | 0.0362 | 0.1047 (Latino) | 0 | n.s. | creates new miRNA binding sites | 1 pediatric CD |
Variants were annotated using the NC_000005.9(NM_000919.3) reference sequence. All variants were observed in heterozygosis. Unless specified, MAFs were retrieved from the gnomAD database ver. 3.1.2. “European” excludes the Finnish population; “African” includes African-American; and “Latino” includes Admixed American. For in silico predictions, the computational verdict was based on the combined outputs of 19 softwares available in Varsome (within parentheses, the first number represents the pathogenic verdicts, the second number represents the uncertain verdicts, and the third number represents the benign verdicts) for all missense variants. For the truncating and 3’UTR variants, we used Alamut predictions; for the regulatory variants, we used Genomatix MatInspector. Individual variant allele frequencies in the study population were compared with the global frequencies reported in gnomAD using the Fisher’s exact test or chi-square test, as appropriate.
acro, acromegaly; CD, Cushing disease; FIPA, familial isolated pituitary adenoma; MAF, minor allele frequency; n.a., not available/applicable; NFPA, non-functioning pituitary adenoma; n.s., not significant; PALcc, catalytic core of peptidyl-α-hydroxyglycine α-amidating lyase; PHMcc, catalytic core of peptidylglycine α-hydroxylating monooxygenase; PRL, prolactinoma; SA, splice acceptor site; TF, transcription factor; VUS, variant of uncertain significance.
†This individual harbors the PAM p.Glu491Asp variant in exon 14.
‡This individual harbors the PAM p.Val49Leu variant in exon 2.
¥This individual harbors the PAM p.Phe31Tyr variant in exon 2 and a somatic heterozygous p.Ser718del variant in the USP8 gene (13).
††This individual is compound heterozygote for p.[His240Tyr];p.[Phe759Ser].
‡‡This individual is compound heterozygote for p.[Gly552Arg];p.[AspD563Gly].
¥¥This individual harbors a somatic heterozygous p.Ser718Pro variant in the USP8 gene (13).
¥¥¥This individual harbors a somatic heterozygous p.Ser718del variant in the USP8 gene (13).
§Somatic hotspot variants in the USP8, BRAF, and USP48 genes were ruled out in this case.
**Allele frequency obtained from gnomAD ver. 2.1.1.