KDM5A

Chr 12p13.33

lysine demethylase 5A

MANE:: ENST00000399788.7

OMIM: 180202 ↗NCBI: 5927 ↗Ensembl ↗

Annotations refreshed 1 month ago.

Predicted protein structure

AlphaFold predicted structure

KDM5A · P29375

v62025-08-01

Predicted Aligned Error matrix for KDM5A — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

70.7/ 100

Confident

1,690 residues

Confidence breakdown

Very high(≥ 90)27%
Confident(70–90)41%
Low(50–70)8%
Very low(< 50)25%

Open interactive 3D viewer

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

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Intellectual disability
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Fetal anomalies
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
DDG2P
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

El Hayek-Chahrour neurodevelopmental disorder
0.63
Intellectual disability
0.56
Seizure
0.44
acute myeloid leukemia
0.39
lung carcinoma
0.37
autism spectrum disorder
0.37
cutaneous melanoma
0.37
hemangioblastoma
0.37
endometrial endometrioid adenocarcinoma
0.37
colorectal adenocarcinoma
0.37

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

Protein function (UniProt)

Lysine-specific demethylase 5A

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity). Seems to act as a transcriptional corepressor for some genes such as MT1F and to favor the proliferation of cancer cells (PubMed:27427228)