SETD1ASET domain containing 1A, histone lysine methyltransferase
Autism Reports / Total Reports
3 / 4Rare Variants / Common Variants
18 / 0Aliases
SETD1A, EPEDD, KMT2F, Set1, Set1AAssociated Syndromes
-Chromosome Band
16p11.2Associated Disorders
-Genetic Category
Rare Single Gene Mutation, SyndromicRelevance to Autism
De novo missense variants in the SETD1A gene were identified in two ASD probands (Yuen et al., 2017), while a de novo likely gene-disruptive variant in this gene was observed in an ASD proband from the SPARK cohort (Feliciano et al., 2019). Kummeling et al., 2020 reported 15 individuals with de novo SETD1A variants presenting with a novel neurodevelopmental syndrome characterized by global developmental delay and/or intellectual disability, behavioral/psychiatric abnormalities, and craniofacial dysmorphisms; 3/14 individuals in this cohort presented with autistic behavior.
Molecular Function
The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily.
Reports related to SETD1A (4 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder | C Yuen RK et al. (2017) | Yes | - |
2 | Support | Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes | Feliciano P et al. (2019) | Yes | - |
3 | Recent Recommendation | Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome | Kummeling J et al. (2020) | No | - |
4 | Support | - | Woodbury-Smith M et al. (2022) | Yes | - |
Rare Variants (18)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
c.109C>T | p.Gln37Ter | stop_gained | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.4409-2A>G | - | splice_site_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.1363G>T | p.Glu455Ter | stop_gained | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.1495C>T | p.Gln499Ter | stop_gained | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.2725G>T | p.Glu909Ter | stop_gained | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.2968C>T | p.Arg990Ter | stop_gained | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.4582-2_4582del | - | splice_site_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.4495T>G | p.Tyr1499Asp | missense_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.252C>T | p.Asp84%3D | synonymous_variant | Unknown | - | - | 35205252 | Woodbury-Smith M et al. (2022) | |
c.2740C>T | p.Pro914Ser | missense_variant | De novo | NA | Simplex | 28263302 | C Yuen RK et al. (2017) | |
c.4246G>A | p.Glu1416Lys | missense_variant | De novo | NA | Multiplex | 28263302 | C Yuen RK et al. (2017) | |
c.1381dup | p.Arg461ProfsTer18 | frameshift_variant | De novo | NA | - | 31452935 | Feliciano P et al. (2019) | |
c.1014dup | p.Ala339ArgfsTer23 | frameshift_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.2289dup | p.Val764SerfsTer61 | frameshift_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.1602_1603del | p.Gly535AlafsTer12 | frameshift_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.3982_3983del | p.Phe1328GlnfsTer5 | frameshift_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.1144_1147del | p.Tyr382HisfsTer114 | frameshift_variant | De novo | NA | - | 32346159 | Kummeling J et al. (2020) | |
c.3937_3947del | p.Pro1313AlafsTer17 | frameshift_variant | Unknown | Not maternal | - | 32346159 | Kummeling J et al. (2020) |
Common Variants
No common variants reported.
CNVs associated with SETD1A(1 CNVs)
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16p11.2 | 125 | Deletion-Duplication | 189 / 1599 |