SETD1A
  • 3
    Haplo
    Score
  • 0
    Triplo
    Score

Gene Facts External Data Attribution

HGNC Symbol
SETD1A (HGNC:29010) HGNC Entrez Ensembl OMIM UCSC Uniprot GeneReviews LOVD LSDB ClinVar
HGNC Name
SET domain containing 1A, histone lysine methyltransferase
Gene type
protein-coding gene
Locus type
gene with protein product
Previous symbols
No previous names found
Alias symbols
KIAA0339, Set1, KMT2F, SET1A
%HI
12.55(Read more about the DECIPHER Haploinsufficiency Index)
pLI
1(Read more about gnomAD pLI score)
LOEUF
0.28(Read more about gnomAD LOEUF score)
Cytoband
16p11.2
Genomic Coordinates
GRCh37/hg19: chr16:30969075-30995985 NCBI Ensembl UCSC
GRCh38/hg38: chr16:30957754-30984664 NCBI Ensembl UCSC
MANE Select Transcript
NM_014712.3 ENST00000262519.14 (Read more about MANE Select)
Function
Histone methyltransferase that catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism (PubMed:25561738, PubMed:12670868). Part of chromatin remodeling machinery, forms H3K4me1, H3K4me2 and H3K4me3 methylation marks at active chromatin sites where transcription and DNA repair take place (PubMed:29937342, PubMed:31197650, PubMed:32346159). Responsible for H3K4me3 enriched promoters and transcriptional p... (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

Dosage ID:
ISCA-19807
ClinGen Curation ID:
CCID:007830
Curation Status:
Complete
Issue Type:
Dosage Curation - Gene
Haploinsufficiency:
Sufficient Evidence for Haploinsufficiency (3)
Read full report...
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Read full report...
Last Evaluated:
02/28/2018

Haploinsufficiency (HI) Score Details

HI Score:
3
HI Evidence Strength:
Sufficient Evidence for Haploinsufficiency (Disclaimer)
HI Disease:
HI Evidence:
  • PUBMED: 24853937
    Takata 2014 reports 2 de novo loss of function mutations among 231 patients with schizophrenia phenotype from exome sequencing data. No loss of function variants found in the 34 controls. The two patients with the mutations also had obsessive compulsive disorder.
  • PUBMED: 26974950
    Singh 2016 investigated several different patient cohorts (schizophrenia and patient groups with developmental delays). In the schizophrenia cohorts, they observed a total of 10 loss-of-function mutations at least 4 of which were de novo. Statistical analysis of case versus controls were significant for elevation of SETD1A LOF mutations. In the developmental delay cohorts, 6 additional LOF mutations were detected. Two had unknown inheritance, 2 were de novo and 2 were maternally inherited without clinical information on the mothers. In total 16 SETD1A LOF of function mutations were identified in patients with at least 6 de novo mutations. Only two LOF mutations observed among 58,404 controls (both in ExAC). Based on the phenotypes of the patients, the full clinical spectrum associated with SETD1A LOF mutations is yet to be determined, but includes schizophrenia, likely developmental delay, and possibly facial dysmorphism, epilepsy and personality disorder.
HI Evidence Comments:
While focal deletions of SETD1A have not been described, emerging evidence demonstrates a clear association between SETD1A LOF mutations and schizophrenia and likely additional neurodevelopmental phenotypes.

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)

Genomic View

Select assembly: (NC_000016.9) (NC_000016.10)