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Relevance to Autism

De novo frameshift variants in the KMT2B were recently reported in two unrelated individuals diagnosed with autism spectrum disorder: the first was from the Children's Neurodevelopmental Center, Hasbro Children's Hospital and also presented with dysmorphic features, developmental delay/intellectual disability, and additional behavioral comorbidities, while the second was from a cohort of 112 Chinese ASD patients and their non-ASD parents from Peking University Sixth Hospital (Chang et al., 2024; Lob et al., 2024). Additional de novo variants in the KMT2B gene, incluiding a de novo nonsense variant, a de novo splice-donor variant, and five de novo missense variants, have been observed in ASD probands from the Autism Sequencing Consortium, the Simons Simplex Collection, the SPARK cohort, and the MSSNG cohort (Iossifov et al., 2014; Yuen et al., 2017; Feliciano et al., 2019; Satterstrom et al., 2020; Zhou et al., 2022; Fu et al., 2022). Heterozygous mutations in the KMT2B gene are also responsible for autosomal dominant intellectual developmental disorder 68 (MRD68; OMIM 619934) and childhood-onset dystonia 28 (DYT28; OMIM 617284). Cif et al., 2020 described a cohort of 53 patients with KMT2B mutations presenting with either dystonia (n=44) or a non-dystonic neurodevelopmental phenotype (n=9); autism spectrum disorder was reported in individuals from both subsets of KMT2B-associated disease.

Molecular Function

This gene encodes a protein which contains multiple domains including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains, and a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain. The SET domain is a conserved C-terminal domain that characterizes proteins of the MLL (mixed-lineage leukemia) family. This gene is ubiquitously expressed in adult tissues.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Genetic Diagnostic Yield in Autism Spectrum Disorder (ASD) and Epilepsy Phenotypes in Children with Genetically Defined ASD
ASD
DD, ID
Support
KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation
Autosomal dominant intellectual developmental diso
ASD, ADHD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Pathogenic variants in chromatin-related genes: Linking immune dysregulation to neuroregression and acute neuropsychiatric disorders
ASD, DD
Support
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
ASD
Support
Variable expressivity of KMT2B variants at codon 2565 in patients with dystonia and developmental disorders
DD, ID, dystonia
ASD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Genomic insights from a deeply phenotyped highly consanguineous neurodevelopmental disorders cohort
DD
ASD or autistic behavior, epilepsy/seizures
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Recent recommendation
Whole-genome sequencing identifies novel genes for autism in Chinese trios
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1466R001 
 frameshift_variant 
 c.6895dup 
 p.Arg2299ProfsTer4 
 De novo 
  
  
 GEN1466R002 
 frameshift_variant 
 c.6754_6755insGC 
 p.Ala2252GlyfsTer10 
 De novo 
  
 Simplex 
 GEN1466R003 
 synonymous_variant 
 c.4368C>T 
 p.Phe1456= 
 De novo 
  
 Simplex 
 GEN1466R004 
 synonymous_variant 
 c.2871C>T 
 p.His957= 
 De novo 
  
 Simplex 
 GEN1466R005 
 synonymous_variant 
 c.4056C>T 
 p.Ser1352= 
 De novo 
  
 Multiplex 
 GEN1466R006 
 missense_variant 
 c.7715C>T 
 p.Thr2572Met 
 De novo 
  
 Multiplex 
 GEN1466R007 
 missense_variant 
 c.3050C>T 
 p.Ala1017Val 
 De novo 
  
  
 GEN1466R008 
 stop_gained 
 c.5335C>T 
 p.Arg1779Ter 
 De novo 
  
  
 GEN1466R009 
 missense_variant 
 c.5475T>G 
 p.Asp1825Glu 
 De novo 
  
 Simplex 
 GEN1466R010 
 inframe_insertion 
 c.11_16dup 
 p.Ala4_Ala5dup 
 De novo 
  
 Simplex 
 GEN1466R011 
 synonymous_variant 
 c.894T>G 
 p.Gly298= 
 De novo 
  
 Simplex 
 GEN1466R012 
 synonymous_variant 
 c.2736G>A 
 p.Ala912= 
 De novo 
  
  
 GEN1466R013 
 splice_site_variant 
 c.2999_3002+6del 
  
 De novo 
  
  
 GEN1466R014 
 missense_variant 
 c.6869C>T 
 p.Pro2290Leu 
 De novo 
  
  
 GEN1466R015 
 missense_variant 
 c.5381A>C 
 p.His1794Pro 
 De novo 
  
  
 GEN1466R016 
 synonymous_variant 
 c.6027C>T 
 p.Ala2009= 
 De novo 
  
  
 GEN1466R017 
 synonymous_variant 
 c.7506G>A 
 p.Pro2502= 
 De novo 
  
  
 GEN1466R018 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN1466R019 
 copy_number_loss 
  
  
 Unknown 
  
  
 GEN1466R020 
 frameshift_variant 
 c.12_24dup 
 p.Ser9GlyfsTer111 
 De novo 
  
  
 GEN1466R021 
 frameshift_variant 
 c.118del 
 p.Ala40ProfsTer6 
 De novo 
  
 Multiplex (monozygotic twins) 
 GEN1466R022 
 frameshift_variant 
 c.816dup 
 p.Gly273ArgfsTer61 
 De novo 
  
  
 GEN1466R023 
 stop_gained 
 c.850C>T 
 p.Gln284Ter 
 De novo 
  
  
 GEN1466R024 
 frameshift_variant 
 c.1107dup 
 p.Glu370ArgfsTer19 
 De novo 
  
  
 GEN1466R025 
 frameshift_variant 
 c.1656dup 
 p.Lys553GlnfsTer46 
 De novo 
  
  
 GEN1466R026 
 frameshift_variant 
 c.2137dup 
 p.Thr713AsnfsTer4 
 Unknown 
 Not maternal 
  
 GEN1466R027 
 stop_gained 
 c.2227_2228delinsTAG 
 p.Ala743Ter 
 Unknown 
  
  
 GEN1466R028 
 stop_gained 
 c.2425C>T 
 p.Gln809Ter 
 De novo 
  
  
 GEN1466R029 
 stop_gained 
 c.2428C>T 
 p.Gln810Ter 
 De novo 
  
  
 GEN1466R030 
 stop_gained 
 c.2434C>T 
 p.Gln812Ter 
 Unknown 
  
  
 GEN1466R031 
 missense_variant 
 c.3014G>A 
 p.Cys1005Tyr 
 De novo 
  
  
 GEN1466R032 
 splice_site_variant 
 c.3058+1G>A 
  
 De novo 
  
  
 GEN1466R033 
 frameshift_variant 
 c.3147_3160del 
 p.Gly1050ProfsTer33 
 Familial 
 Maternal 
  
 GEN1466R034 
 frameshift_variant 
 c.3325del 
 p.Arg1109GlufsTer73 
 Unknown 
  
 Multiplex 
 GEN1466R035 
 stop_gained 
 c.3592_3626del 
 p.Gly1198GlnfsTer14 
 De novo 
  
  
 GEN1466R036 
 frameshift_variant 
 c.3602del 
 p.Pro1201ArgfsTer154 
 De novo 
  
  
 GEN1466R037 
 splice_site_variant 
 c.3642+5G>A 
  
 De novo 
  
  
 GEN1466R038 
 frameshift_variant 
 c.3997del 
 p.Glu1333ArgfsTer22 
 Unknown 
 Not maternal 
  
 GEN1466R039 
 stop_gained 
 c.4760dup 
 p.Tyr1587Ter 
 Unknown 
  
  
 GEN1466R040 
 stop_gained 
 c.4760dup 
 p.Tyr1587Ter 
 De novo 
  
  
 GEN1466R041 
 missense_variant 
 c.4789C>T 
 p.Arg1597Trp 
 De novo 
  
  
 GEN1466R042 
 inframe_deletion 
 c.4825_4827del 
 p.Val1609del 
 De novo 
  
  
 GEN1466R043 
 missense_variant 
 c.4847C>T 
 p.Ala1616Val 
 De novo 
  
  
 GEN1466R044 
 missense_variant 
 c.4931G>T 
 p.Cys1644Phe 
 De novo 
  
  
 GEN1466R045 
 missense_variant 
 c.4960T>C 
 p.Cys1654Arg 
 Familial 
 Maternal 
  
 GEN1466R046 
 frameshift_variant 
 c.5230_5233del 
 p.Ser1744IlefsTer150 
 Unknown 
 Not maternal 
  
 GEN1466R047 
 frameshift_variant 
 c.5658del 
 p.Ser1887ProfsTer8 
 De novo 
  
  
 GEN1466R048 
 frameshift_variant 
 c.5682del 
 p.Thr1895ProfsTer39 
 Unknown 
  
  
 GEN1466R049 
 frameshift_variant 
 c.5724_5751del 
 p.Pro1909LeufsTer16 
 De novo 
  
  
 GEN1466R050 
 frameshift_variant 
 c.6090dup 
 p.Thr2031HisfsTer29 
 De novo 
  
  
 GEN1466R051 
 frameshift_variant 
 c.6245_6266dup 
 p.Val2090HisfsTer25 
 De novo 
  
  
 GEN1466R052 
 stop_gained 
 c.6439C>T 
 p.Gln2147Ter 
 De novo 
  
  
 GEN1466R053 
 splice_site_variant 
 c.7297+1G>A 
  
 De novo 
  
  
 GEN1466R054 
 splice_site_variant 
 c.7298-1G>A 
  
 De novo 
  
  
 GEN1466R055 
 stop_gained 
 c.7348C>T 
 p.Arg2450Ter 
 Unknown 
 Not maternal 
  
 GEN1466R056 
 frameshift_variant 
 c.7614del 
 p.Thr2539ProfsTer75 
 De novo 
  
  
 GEN1466R057 
 stop_gained 
 c.7759C>T 
 p.Arg2587Ter 
 De novo 
  
  
 GEN1466R058 
 missense_variant 
 c.7943C>T 
 p.Ala2648Val 
 Unknown 
 Not maternal 
  
 GEN1466R059 
 missense_variant 
 c.7945C>T 
 p.Arg2649Cys 
 Unknown 
  
  
 GEN1466R060 
 frameshift_variant 
 c.1127_1130del 
 p.Lys376ArgfsTer10 
 De novo 
  
  
 GEN1466R061 
 missense_variant 
 c.3665G>A 
 p.Cys1222Tyr 
 De novo 
  
  
 GEN1466R062 
 stop_gained 
 c.3885G>A 
 p.Trp1295Ter 
 De novo 
  
  
 GEN1466R063 
 missense_variant 
 c.4789C>T 
 p.Arg1597Trp 
 De novo 
  
  
 GEN1466R064 
 missense_variant 
 c.5046C>G 
 p.Cys1682Trp 
 De novo 
  
  
 GEN1466R065 
 frameshift_variant 
 c.6895dup 
 p.Arg2299ProfsTer4 
 De novo 
  
  
 GEN1466R066 
 frameshift_variant 
 c.7271dup 
 p.Ser2425GlnfsTer3 
 De novo 
  
  
 GEN1466R067a 
 missense_variant 
 c.479C>T 
 p.Pro160Leu 
 Unknown 
  
  
 GEN1466R067b 
 missense_variant 
 c.573G>T 
 p.Gln191His 
 Unknown 
  
  
 GEN1466R068 
 missense_variant 
 c.6683C>A 
 p.Ala2228Asp 
 Unknown 
  
  
 GEN1466R069 
 missense_variant 
 c.4198C>T 
 p.Arg1400Cys 
 Unknown 
  
  
 GEN1466R070 
 missense_variant 
 c.7693C>G 
 p.Arg2565Gly 
 Familial 
 Paternal 
 Simplex 
 GEN1466R071 
 missense_variant 
 c.7693C>G 
 p.Arg2565Gly 
 Unknown 
  
 Multiplex 
 GEN1466R072 
 missense_variant 
 c.7693C>T 
 p.Arg2565Cys 
 De novo 
  
 Simplex 
 GEN1466R073 
 frameshift_variant 
 c.7288_7292dup 
 p.Glu2432AlafsTer9 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
19
Deletion
 13
 

No Animal Model Data Available

No PIN Data Available
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