De novo EHMT2 variants cause an autosomal dominant EHMT2-related Kleefstra syndrome via loss of G9a methyltransferase activity

A Aleš Hnízda B Beatriz Martinez-Delgado D Diana Sánchez-Ponce J Javier Alonso J Jeanne Amiel T Tania Attie-Bitach A Ariadna Bada-Navarro B Beatriz Baladron E Eva Bermejo-Sanchez V Vítězslav Brinsa I Ivana Buková R Rosario Cazorla-Calleja S Sylvie Červenková S Shanshan Chow P Petr Dušek O Olha Fedosieieva M Marta Fernandez-Prieto S Sourav Ghosh G Gema Gomez-Mariano A Andrea Gřegořová M Mark James Hamilton H Hana Hartmannová E Esther Hernandez-SanMiguel M Marina Herrero-Matesanz K Kateřina Hodaňová A Alan Kádek J Jennifer Kerkhof T Tjitske Kleefstra D Didier Lacombe M Michael A. Levy E Estrella Lopez-Martin R Ruaud Lyse P Petr Man P Purificacion Marin-Reina E Ellen F. Macnamara H Haley McConkey P Petra Melenovská L Lidia M. Mielu D David Moore L Lenka Steiner Mrázová K Karolína Musilová K Kristýna Neffeová P Petr Nickl D David Pajuelo Reguera M Martina Pavlíková L Lea Pavlovičová M Manuel Posada J Jan Procházka K Kateryna Pysanenko S Sheila Ramos del Saz D Dmitrijs Rots J Jessica Rzasa R Radislav Sedláček V Viktor Stránecký F František Špoutil M Matthew L. Tedder L Louise Thompson C Cynthia J. Tifft (Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD) F Frederic Tran Mau-Them H Helena Trešlová A Antonio Vitobello S Sarah Hilton C Christopher Campbell S Siddharth Banka D Daniel Jirák B Bekim Sadikovic J Jakub Sikora S Stanislav Kmoch M Maria J. Barrero L Lenka Nosková

Abstract

Abstract EHMT1 and EHMT2 genes encode human euchromatin histone lysine methyltransferase 1 and 2 (EHMT1 alias GLP; EHMT2 alias G9a) that form heteromeric GLP/G9a complexes with essential roles in epigenetic regulation of gene expression. While EHMT1 haploinsufficiency has been established as the cause of Kleefstra syndrome 1, the pathogenesis of G9a dysfunction in human disease remains largely unknown. We identified seven de novo EHMT2 variants in patients with clinical presentation, episignatures, histone modifications and transcriptomic profiles similar to those of Kleefstra syndrome 1. In vitro studies reveal that these variants encode for structurally stable G9a proteins that are catalytically incompetent due to aberrant interactions either with histone H3 tail or with S-adenosylmethionine. Heterozygous mice carrying a patient-derived variant exhibit growth retardation, facial/skull dysmorphia and aberrant behavior. Here we report pathogenic EHMT2 variants that likely exert dominant-negative effect on GLP/G9a complexes and thus genocopy the EHMT1 haploinsufficiency via a distinct molecular mechanism, defining an autosomal dominant EHMT2 -related Kleefstra syndrome.

Article Details

Volume / Issue Vol. 1, Issue 1
Published July 01, 2026
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio

ISSN: 2041-1723 Open Access Life Sciences

Authors (70)

A

Aleš Hnízda

B

Beatriz Martinez-Delgado

D

Diana Sánchez-Ponce

J

Javier Alonso

J

Jeanne Amiel

T

Tania Attie-Bitach

A

Ariadna Bada-Navarro

B

Beatriz Baladron

E

Eva Bermejo-Sanchez

V

Vítězslav Brinsa

I

Ivana Buková

R

Rosario Cazorla-Calleja

S

Sylvie Červenková

S

Shanshan Chow

P

Petr Dušek

O

Olha Fedosieieva

M

Marta Fernandez-Prieto

S

Sourav Ghosh

G

Gema Gomez-Mariano

A

Andrea Gřegořová

M

Mark James Hamilton

H

Hana Hartmannová

E

Esther Hernandez-SanMiguel

M

Marina Herrero-Matesanz

K

Kateřina Hodaňová

A

Alan Kádek

J

Jennifer Kerkhof

T

Tjitske Kleefstra

D

Didier Lacombe

M

Michael A. Levy

E

Estrella Lopez-Martin

R

Ruaud Lyse

P

Petr Man

P

Purificacion Marin-Reina

E

Ellen F. Macnamara

H

Haley McConkey

P

Petra Melenovská

L

Lidia M. Mielu

D

David Moore

L

Lenka Steiner Mrázová

K

Karolína Musilová

K

Kristýna Neffeová

P

Petr Nickl

D

David Pajuelo Reguera

M

Martina Pavlíková

L

Lea Pavlovičová

M

Manuel Posada

J

Jan Procházka

K

Kateryna Pysanenko

S

Sheila Ramos del Saz

D

Dmitrijs Rots

J

Jessica Rzasa

R

Radislav Sedláček

V

Viktor Stránecký

F

František Špoutil

M

Matthew L. Tedder

L

Louise Thompson

C

Cynthia J. Tifft

Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD

F

Frederic Tran Mau-Them

H

Helena Trešlová

A

Antonio Vitobello

S

Sarah Hilton

C

Christopher Campbell

S

Siddharth Banka

D

Daniel Jirák

B

Bekim Sadikovic

J

Jakub Sikora

S

Stanislav Kmoch

M

Maria J. Barrero

L

Lenka Nosková