배경: 가성부갑상선기능저하증 1b형(PHP-1b)은 드문 각인 장애로, 신장에서 부갑상선 호르몬 저항성을 특징으로 하지만, Al-bright 유전성 골이영양증의 신체적 특징은 나타나지 않는다. 이전에 보고된 바에 따르면, 여러 비관련 환자들에서 공통적으로 나타나는 이형접합성 3kb STX16 결실이 있다. 이 결실은 GNAS 유전자 A/B 엑손에서 메틸화 문제를 유발한다. 저자들은 STX16 결실과 정확한 절단점을 확인하여 STX16 결실의 메커니즘을 규명하고자 하였다.
방법: 저자들은 PHP-1b로 진단받았으나 GNAS 유전자에 병원성 서열 변이가 없는 10명의 환자를 대상으로 연구하였다. STX16의 복제수를 평가하기 위해 메틸화 특이적 복합결찰 의존 탐침 증폭법(methylation-specific multiplex ligation-dependent probe am-plification, MS-MLPA) 분석을 수행하였다. 절단점 부근에서의 PCR과 생거 시퀀싱을 통해 정확한 절단점을 결정했다.
결과: 10명의 환자 중 2명(20%)에서 STX16 유전자 결실이 확인되었다. 두 환자의 결실 범위는 g.57,243,566에서 g.57,246,545까지로 동일했으며, 이는 이전 보고와 일치하는 2,979 bp에 해당한다 (2009년 2월 인간 참조 서열 hg19, build37 기준).
결론: 5′ 및 3′ 절단점은 mammalian-wide interspersed repeats (MIRs) 내에 위치해 있으며, 이는 STX16의 일반적인 3-kb 결실에 대한 가설적 메커니즘으로서 MIRs 매개 비대립동종재조합(non-allelic homologous recombination, NAHR)을 시사한다. 저자들이 아는 한, 이 연구는 MIR가 유전체 재배열에 관여한다는 것을 처음으로 보여준 연구이다.
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Original Article
가성부갑상샘저하증에서 STX16 유전자 결실의 유전적 특성 규명
Genomic Characterization of STX16 Deletion in Pseudohypoparathyroidism
서울대학교병원 임상유전체의학1서울대학교병원 진단검사의학과2, 서울대학교 암연구소3
Man Jin Kim, M.D.1, Jee-Soo Lee, M.D.2, Sung Im Cho, M.S.2, Moon-Woo Seong, M.D. 
2,3
2,3Department of Genomic Medicine1, Seoul National University Hospital, Seoul; Department of Laboratory Medicine2, Seoul National University Hospital, Seoul National University College of Medicine, Seoul; Cancer Research Institute3, Seoul National University, Seoul, Korea
Correspondence to:Received: May 21, 2024; Revised: August 19, 2024; Accepted: August 19, 2024
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Lab Med Online 2024; 14(4): 364-368
Published October 1, 2024 https://doi.org/10.47429/lmo.2024.14.4.364
Copyright © The Korean Society for Laboratory Medicine.
Background: Pseudohypoparathyroidism type Ib (PHP-1b) is a rare imprinting disorder characterized by renal parathyroid hormone resistance, but without the physical features of Albright hereditary osteodystrophy. A common heterozygous 3-kb deletion of STX16 was previously reported in multiple unrelated probands. This deletion causes isolated loss of methylation at GNAS exons A/B. We aimed to identify STX16 deletions and the exact breakpoints to gain insights into the mechanism of STX16 deletion.
Methods: We investigated 10 patients who were diagnosed with pseudohypoparathyroidism type Ib, but did not have any pathogenic variants in GNAS. A methylation-specific multiplex ligation-dependent probe amplification assay of STX16 was performed to assess allelic dosage. Junction PCR and Sanger sequencing were performed around the presumptive breakpoint area to determine the exact breakpoint.
Results: STX16 gene deletion was detected in two of the 10 probands (20%). The deletion range was the same for both probands, ranging from g.57,243,566 to g.57,246,545 (2,979 bp), according to the February 2009 human reference sequence (hg19, build37), which is consistent with previous reports. The 5’ and 3’ break points were located in the mammalian-wide interspersed repeats (MIRs) sequences suggesting MIR-mediated non-allelic homologous recombination as the putative mechanism for the common STX16 3-kb deletion.
Conclusions: Non-allelic homologous recombination is a putative mechanism of STX16 deletion in our patients. To the best of our knowledge, this is the first study to show that MIRs are involved in genomic rearrangements.
Methods: We investigated 10 patients who were diagnosed with pseudohypoparathyroidism type Ib, but did not have any pathogenic variants in GNAS. A methylation-specific multiplex ligation-dependent probe amplification assay of STX16 was performed to assess allelic dosage. Junction PCR and Sanger sequencing were performed around the presumptive breakpoint area to determine the exact breakpoint.
Results: STX16 gene deletion was detected in two of the 10 probands (20%). The deletion range was the same for both probands, ranging from g.57,243,566 to g.57,246,545 (2,979 bp), according to the February 2009 human reference sequence (hg19, build37), which is consistent with previous reports. The 5’ and 3’ break points were located in the mammalian-wide interspersed repeats (MIRs) sequences suggesting MIR-mediated non-allelic homologous recombination as the putative mechanism for the common STX16 3-kb deletion.
Conclusions: Non-allelic homologous recombination is a putative mechanism of STX16 deletion in our patients. To the best of our knowledge, this is the first study to show that MIRs are involved in genomic rearrangements.
Keywords
Pseudohypoparathyroidism, Gene rearrangement, DNA copy number variations, STX16
