SETD1A

Chr 16p11.2

SET domain containing 1A, histone lysine methyltransferase

Aliases:: KIAA0339, Set1, KMT2F, SET1A
MANE:: ENST00000262519.14

OMIM: 611052 ↗NCBI: 9739 ↗Ensembl ↗

Annotations refreshed 9 hours ago.

Predicted protein structure

AlphaFold predicted structure

SETD1A · O15047

v62025-08-01

Predicted Aligned Error matrix for SETD1A — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

48.3/ 100

Very low

1,707 residues

Confidence breakdown

Very high(≥ 90)9%
Confident(70–90)14%
Low(50–70)8%
Very low(< 50)69%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

DDG2P
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Fetal anomalies
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Disease associations (Open Targets)

neurodevelopmental disorder with speech impairment and dysmorphic facies
0.76
epilepsy, early-onset, with or without developmental delay
0.73
schizophrenia
0.58
hereditary disease
0.53
Intellectual disability
0.49
neurodevelopmental disorder
0.39
complex neurodevelopmental disorder
0.37
neurodevelopmental disorder with dysmorphic facies and distal limb anomalies
0.34
autism spectrum disorder
0.27
developmental disability
0.15

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Histone-lysine N-methyltransferase SETD1A

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:12670868, PubMed:25561738). 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 programming of inner mass stem cells and neuron progenitors during embryogenesis (By similarity) (PubMed:31197650). Required for H3K4me1 mark at stalled replication forks. Mediates FANCD2-dependent nucleosome remodeling and RAD51 nucleofilaments stabilization at reversed forks, protecting them from nucleolytic degradation (PubMed:29937342, PubMed:32346159). Does not methylate 'Lys-4' of histone H3 if the neighboring 'Lys-9' residue is already methylated (PubMed:12670868). Binds RNAs involved in RNA processing and the DNA damage response (PubMed:38003223)

Curated MONDO disease pages that list SETD1A among their top associated genes.

schizophreniaRare

Predicted protein structure

Clinical relevance (Genomics England PanelApp)

Disease associations (Open Targets)

Protein function (UniProt)

Diseases associated with SETD1A