Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders

Tarjinder Singh, Mitja I. Kurki, David Curtis, Shaun M. Purcell, Lucy Crooks, Jeremy McRae, Jaana Suvisaari, Himanshu Chheda, Douglas Blackwood, Gerome Breen, Olli Pietilinen, Sebastian S. Gerety, Muhammad Ayub, Moira Blyth, Trevor Cole, David Collier, Eve L. Coomber, Nick Craddock, Mark J. Daly, John DaneshMarta DiForti, Alison Foster, Nelson B. Freimer, Daniel Geschwind, Mandy Johnstone, Shelagh Joss, Georg Kirov, Jarmo Körkkö, Outi Kuismin, Peter Holmans, Christina M. Hultman, Conrad Iyegbe, Jouko Lönnqvist, Minna Mnnikkö, Steve A. McCarroll, Peter McGuffin, Andrew M. McIntosh, Andrew McQuillin, Jukka S. Moilanen, Carmel Moore, Robin M. Murray, Ruth Newbury-Ecob, Willem Ouwehand, Tiina Paunio, Elena Prigmore, Elliott Rees, David Roberts, Jennifer Sambrook, Pamela Sklar, David St Clair, Juha Veijola, James T R Walters, Hywel Williams, Patrick F. Sullivan, Matthew E. Hurles, Michael C. O'Donovan, Aarno Palotie, Michael J. Owen, Jeffrey C. Barrett*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

306 Citations (Scopus)


By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10 -9). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.

Original languageEnglish
Pages (from-to)571-577
Number of pages7
JournalNature Neuroscience
Issue number4
Early online date14 Mar 2016
Publication statusPublished - 29 Mar 2016


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