Human Gene Module / Chromosome 19 / DOT1L

DOT1LDOT1 like histone lysine methyltransferase

SFARI Gene Score
2S
Strong Candidate, Syndromic Criteria 2.1, Syndromic
Autism Reports / Total Reports
4 / 6
Rare Variants / Common Variants
30 / 0
Aliases
-
Associated Syndromes
Nil-Deshwan neurodevelopmental syndrome, DD
Chromosome Band
19p13.3
Associated Disorders
-
Relevance to Autism

Maroni et al., 2025 identified a cohort of 16 individuals through collaborating clinicians and GeneMatcher with monoallelic DOT1L variants presenting with a variable neurodevelopmental disorder characterized by language delay (13/16), motor delay (9/16), intellectual disability (4/16), a diagnosis of ASD (4/16), seizures/epilepsy (3/16), and craniofacial anomalies (14/16); additional functional studies in this report identified patient-specific missense variants with either decreased (the newly identified p.Asp157Asn variant) or increased (the previously reported p.Glu123Lys variant) methyltransferase activity, while heterozygous forebrain-specific Dot1l conditional knockout mice demonstrated altered early vocalization development in both male and female pups, as well as a sex-specific sociability deficit in the three-chamber test in female Dot1l cKO mice. A previous study (Nil et al., 2023) had reported nine unrelated individuals with seven different de novo heterozygous missense variants in DOT1L through the Undiagnosed Disease Network (UDN), the SickKids Complex Care genomics project, and GeneMatcher presenting with some degree of global developmental delay/intellectual disability and at least one major congenital anomaly in most individuals; subsequent functional assessment of DOT1L missense variants in Drosophila and human cells in this report demonstrated gain-of-function effects in flies and increased H3K79 methylation levels in flies and human cells. A number of de novo DOT1L variants, including two de novo loss-of-function variants in probands from the Simons Simplex Collection, have been reported in ASD probands (Iossifov et al., 2014; Satterstrom et al., 2020; Zhou et al., 2022; Fu et al., 2022).

Molecular Function

The protein encoded by this gene is a histone methyltransferase that methylates lysine-79 of histone H3. It is inactive against free core histones, but shows significant histone methyltransferase activity against nucleosomes.

SFARI Genomic Platforms
Reports related to DOT1L (6 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
3 Support - Zhou X et al. (2022) Yes -
4 Support - Fu JM et al. (2022) Yes -
5 Support - Zelha Nil et al. (2023) No ASD, epilepsy/seizures
6 Primary - Marissa J Maroni et al. () No ASD, ADHD, ID, epilepsy/seizures
Rare Variants   (30)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1399G>A p.Val467Met missense_variant De novo - - 35982160 Fu JM et al. (2022)
c.133T>G p.Cys45Gly missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.1792C>T p.Gln598Ter stop_gained Unknown - - 40494548 Marissa J Maroni et al. ()
c.299C>T p.Thr100Met missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.367G>A p.Glu123Lys missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.367G>A p.Glu123Lys missense_variant Unknown - - 37827158 Zelha Nil et al. (2023)
c.385G>A p.Glu129Lys missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.1348C>T p.Gln450Ter stop_gained De novo - Simplex 35982159 Zhou X et al. (2022)
c.1876C>G p.Leu626Val missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.2557C>T p.Arg853Cys missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.3074A>T p.Lys1025Met missense_variant De novo - - 37827158 Zelha Nil et al. (2023)
c.121A>T p.Ile41Phe missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.123C>G p.Ile41Met missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.255C>G p.Ile85Met missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.400G>A p.Glu134Lys missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.409G>A p.Gly137Arg missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.469G>A p.Asp157Asn missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.469G>T p.Asp157Tyr missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.565G>A p.Asp189Asn missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.806C>T p.Ser269Leu missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.995C>G p.Pro332Arg missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.1262A>G p.Asn421Ser missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.2075T>G p.Leu692Arg missense_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.1822C>T p.Gln608Ter stop_gained De novo - Simplex 25363768 Iossifov I et al. (2014)
- p.Leu1067AspfsTer66 frameshift_variant Unknown - - 40494548 Marissa J Maroni et al. ()
c.2822G>C p.Gly941Ala missense_variant De novo - Unknown 35982159 Zhou X et al. (2022)
c.2610G>A p.Pro870= synonymous_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.4432C>T p.Pro1478Ser missense_variant De novo - Simplex 35982159 Zhou X et al. (2022)
c.1344A>C p.Ser448= synonymous_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.1624_1626del p.Glu542del inframe_deletion Unknown - - 40494548 Marissa J Maroni et al. ()
Common Variants  

No common variants reported.

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