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Relevance to Autism

Shangguan et al., 2025 assembled genotype and phenotype data for 9 affected individuals from 9 unrelated families with predicted deleterious KMT2D variants through literature (Parisi et al., 2015; Sertelik et al., 2016; Luo et al., 2021) and two web-based databases (ClinVar and DECIPHER); all 9 probands were diagnosed with autism and presented with intellectual disability and dysmorphic facial features. In the same report, the authors observed that selective knockdown of Kmt2d in the mouse hippocampus resulted in defects in social behaviors and increased repetitive behavior, as well as decreased excitatory and increased inhibitory synaptic transmission. De novo variants in the KMT2D gene, including a loss-of-function variant and several potentially deleterious missense variants, have also been identified in ASD probands from the Simons Simplex Collection, the SPARK cohort, the Autism Sequencing Consortium, the MSSNG cohort, and a Korean ASD cohort (Iossifov et al., 2014; Yuen et al., 2017; Krupp et al., 2017; Satterstrom et al., 2020; Zhou et al., 2022; Kim et al., 2024; Tan et al., 2024).

Molecular Function

The protein encoded by this gene is a histone methyltransferase that methylates the Lys-4 position of histone H3. The encoded protein is part of a large protein complex called ASCOM, which has been shown to be a transcriptional regulator of the beta-globin and estrogen receptor genes. Mutations in this gene have been shown to be a cause of Kabuki syndrome.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Deficiency of KMT2D causes autistic-like behavior in mice and zebrafish
ASD, ID
Support
Monoallelic loss-of-function variants in GSK3B lead to autism and developmental delay
ASD
Support
Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder.
ASD
Support
Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism
ASD
Support
A Child with Kabuki Syndrome and Autism Spectrum Disorder
Kabuki syndrome 1, ASD, DD, ID, epilepsy/seizures
Support
NGS Custom Panel Implementation in Patients with Non-Syndromic Autism Spectrum Disorders in the Clinical Routine of a Tertiary Hospital
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Autism spectrum disorder in Kabuki syndrome: clinical, diagnostic and rehabilitative aspects assessed through the presentation of three cases
Kabuki syndrome 1, ASD, DD, ID
Support
[Analysis of clinical manifestation and a mosaic frameshift variant of the KMT2D gene in a Chinese patient with Kabuki syndrome]
Kabuki syndrome 1, ASD, DD, ID
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Multilayered genetic dissection of autism: insights from whole-exome sequencing, molecular karyotyping, and cytogenetic analyses in a small Turkish cohort
ASD
Support
Family-based exome sequencing and case-control analysis implicate CEP41 as an ASD gene.
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1522R001 
 frameshift_variant 
 c.1769dupT 
 p.Met590fs 
 Familial 
 Maternal 
  
 GEN1522R002 
 frameshift_variant 
 c.1530del 
 p.Pro511LeufsTer419 
 De novo 
  
  
 GEN1522R003 
 frameshift_variant 
 c.6597del 
 p.Pro2200LeufsTer64 
 De novo 
  
  
 GEN1522R004 
 stop_gained 
 c.9397C>T 
 p.Gln3133Ter 
 De novo 
  
  
 GEN1522R005 
 missense_variant 
 c.15634G>C 
 p.Ala5212Pro 
 De novo 
  
 Simplex 
 GEN1522R006 
 frameshift_variant 
 c.13058delG 
 p.Pro4353ArgfsTer31 
 De novo 
  
  
 GEN1522R007 
 missense_variant 
 c.16529A>G 
 p.Tyr5510Cys 
 De novo 
  
 Simplex 
 GEN1522R008 
 synonymous_variant 
 c.4389C>T 
 p.Thr1463= 
 De novo 
  
 Multiplex 
 GEN1522R009 
 missense_variant 
 c.3103C>A 
 p.Gln1035Lys 
 De novo 
  
 Multiplex 
 GEN1522R010 
 missense_variant 
 c.7753G>C 
 p.Gly2585Arg 
 De novo 
  
 Simplex 
 GEN1522R011 
 missense_variant 
 c.15928G>A 
 p.Gly5310Arg 
 De novo 
  
  
 GEN1522R012 
 missense_variant 
 c.181G>A 
 p.Gly61Ser 
 De novo 
  
  
 GEN1522R013 
 synonymous_variant 
 c.13398A>G 
 p.Leu4466= 
 De novo 
  
 Multiplex 
 GEN1522R014 
 synonymous_variant 
 c.12066G>T 
 p.Thr4022= 
 De novo 
  
 Unknown 
 GEN1522R015 
 missense_variant 
 c.5356C>T 
 p.Arg1786Cys 
 De novo 
  
 Simplex 
 GEN1522R016 
 missense_variant 
 c.1712G>A 
 p.Arg571His 
 De novo 
  
 Simplex 
 GEN1522R017 
 missense_variant 
 c.14653G>T 
 p.Ala4885Ser 
 De novo 
  
  
 GEN1522R018 
 splice_site_variant 
 C>T 
 p.? 
 De novo 
  
 Simplex 
 GEN1522R019 
 missense_variant 
 c.8156G>C 
 p.Ser2719Thr 
 Familial 
  
 Extended multiplex 
 GEN1522R020 
 missense_variant 
 c.13885A>C 
 p.Thr4629Pro 
 Unknown 
  
  
 GEN1522R021 
 missense_variant 
 c.1721C>T 
 p.Pro574Leu 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
12
Duplication
 1
 

No Animal Model Data Available

No PIN Data Available
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