KDM2A

lysine demethylase 2A, the group of F-box and leucine rich repeat proteins|Zinc fingers CXXC-type|Lysine demethylases|PHD finger proteins

Basic information

Region (hg38): 11:67119263-67258082

Previous symbols: [ "FBXL11" ]

Links

ENSG00000173120 ∙ NCBI:22992 ∙ OMIM:605657 ∙ HGNC:13606 ∙ Uniprot:Q9Y2K7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KDM2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM2A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in KDM2A

This is a list of pathogenic ClinVar variants found in the KDM2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-67181328-G-A		not specified	Uncertain significance (May 11, 2022)
11-67181337-A-G		not specified	Uncertain significance (Jan 26, 2022)
11-67215343-G-T		not specified	Uncertain significance (Jan 24, 2024)
11-67215378-G-C		not specified	Uncertain significance (May 30, 2024)
11-67219296-C-T		Neurodevelopmental disorder	Likely pathogenic (Oct 09, 2024)
11-67228119-G-A		not specified	Uncertain significance (Jul 26, 2024)
11-67228132-T-C			Benign (Apr 24, 2019)
11-67231619-C-G		not specified	Uncertain significance (Jan 31, 2024)
11-67231728-G-T		not specified	Uncertain significance (Aug 01, 2022)
11-67231765-C-G		not specified	Uncertain significance (May 20, 2024)
11-67231777-C-A			Likely benign (Mar 01, 2024)
11-67243039-C-G		not specified	Uncertain significance (Feb 22, 2023)
11-67245301-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-67246001-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-67246092-G-C		not specified	Uncertain significance (Apr 07, 2022)
11-67250113-G-C		not specified	Uncertain significance (Sep 22, 2023)
11-67250140-C-G		not specified	Uncertain significance (Jun 17, 2024)
11-67250219-T-G		not specified	Uncertain significance (Apr 09, 2022)
11-67250302-A-C		not specified	Uncertain significance (Dec 05, 2024)
11-67250313-G-T		not specified	Uncertain significance (Jul 07, 2024)
11-67250328-G-T		not specified	Uncertain significance (Sep 01, 2021)
11-67250468-C-T		not specified	Uncertain significance (Oct 27, 2023)
11-67250515-C-G		not specified	Uncertain significance (Jan 18, 2022)
11-67250530-C-T		not specified	Uncertain significance (Nov 25, 2024)
11-67250558-G-A		not specified	Uncertain significance (Jan 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM2A	protein_coding	protein_coding	ENST00000529006	20	138819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.03e-11	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.31	302	696	0.434	0.0000428	7615
Missense in Polyphen		40	261.68	0.15286		2818
Synonymous	-0.410	260	252	1.03	0.0000142	2247
Loss of Function	7.50	0	65.5	0.00	0.00000416	676

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:19001877, ECO:0000269|PubMed:28262558}.
• Pathway: The oncogenic action of Succinate;The oncogenic action of Fumarate;The oncogenic action of 2-hydroxyglutarate;The oncogenic action of L-2-hydroxyglutarate in Hydroxygluaricaciduria;The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria ;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.0344
• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.76

Haploinsufficiency Scores

• pHI: 0.417
• hipred: Y
• hipred_score: 0.728
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kdm2a
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: kdm2aa
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: present

Gene ontology

• Biological process: double-strand break repair via nonhomologous end joining;regulation of transcription by RNA polymerase II;oxidation-reduction process;histone H3-K36 demethylation
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;histone demethylase activity;histone demethylase activity (H3-K36 specific)