KDM2A

Chr 11q13.2

lysine demethylase 2A

Aliases:: KIAA1004, FBL11, LILINA, DKFZP434M1735, FBL7
MANE:: ENST00000529006.7

OMIM: 605657 ↗NCBI: 22992 ↗Ensembl ↗

Annotations refreshed 10 hours ago.

Predicted protein structure

AlphaFold predicted structure

KDM2A · Q9Y2K7

v62025-08-01

Predicted Aligned Error matrix for KDM2A — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

73.3/ 100

Confident

1,162 residues

Confidence breakdown

Very high(≥ 90)48%
Confident(70–90)17%
Low(50–70)4%
Very low(< 50)31%

Open interactive 3D viewer

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

Clinical relevance (Genomics England PanelApp)

Moderate Evidence (Amber)

Early onset or syndromic epilepsy
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Disease associations (Open Targets)

neurodegenerative disease
0.56
neurodevelopmental disorder
0.41
temporomandibular joint disorder
0.24
Abnormality of the skeletal system
0.21
skin disorder
0.19
Alzheimer disease
0.18
prostate carcinoma
0.17
breast cancer
0.11
breast carcinoma
0.11
osteoarthritis, knee
0.10

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

Protein function (UniProt)

Lysine-specific demethylase 2A

Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. Regulates circadian gene expression by repressing the transcriptional activator activity of CLOCK-BMAL1 heterodimer and RORA in a catalytically-independent manner (PubMed:26037310)