Pseudohypoparathyroidism type 1B (PHP1B) is a multihormone resistance disorder caused by aberrant
GNAS
methylation. Characteristic epigenetic changes at
GNAS
differentially methylated regions (DMRs), i.e., NESP, AS1, AS2, XL, and A/B, are associated with specific structural defects in different autosomal dominant PHP1B (AD-PHP1B) subtypes. However, mechanisms underlying abnormal
GNAS
methylation remain incompletely defined, largely because viable PHP1B mouse models are lacking. Using lymphoblastoid cells and induced pluripotent stem cells, we show that various
GNAS
methylation patterns in PHP1B reflect differential disruption of sense and antisense
GNAS
transcripts. In cases with broad
GNAS
methylation changes, loss of the maternal, sense-transcribed exon H/AS region impairs methylation of the AS1 DMR, which results in biallelic expression of an antisense transcript,
GNAS-AS1
, and NESP hypermethylation. In contrast, cases with normal AS1 methylation, including
STX16
deletions, show monoallelic
GNAS-AS1
expression and normal NESP methylation. The roles of these
GNAS
transcripts were confirmed by a retrotransposon in
GNAS-AS1
intron 1, identified in an AD-PHP1B family. This insertion impaired exon H/AS transcription when located on the maternal allele, thus preventing the complete establishment of methylation at all maternal
GNAS
DMRs, leading to biallelic
GNAS-AS1
transcription. However, maternal
GNAS-AS1
transcription was profoundly attenuated, thus allowing only a small gain-of-methylation at NESP. Likewise, on the paternal allele, the retrotransposon attenuated
GNAS-AS1
transcription, thus preventing complete NESP methylation. Our findings support a model of bidirectional transcription-mediated regulation of methylation at
GNAS
DMRs and will help to refine systematic approaches for establishing molecular defects underlying different PHP1B subtypes.