KDM2B

lysine demethylase 2B, the group of F-box and leucine rich repeat proteins|PHD finger proteins|Zinc fingers CXXC-type|Lysine demethylases|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:121429095-121581023

Previous symbols: [ "FBXL10" ]

Links

ENSG00000089094 ∙ NCBI:84678 ∙ OMIM:609078 ∙ HGNC:13610 ∙ Uniprot:Q8NHM5 ∙ 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 KDM2B gene.

• not provided (34 variants)
• Inborn genetic diseases (33 variants)
• KDM2B-related condition (5 variants)
• Global developmental delay;Microcephaly;Hypotonia;Infantile spasms (1 variants)
• not specified (1 variants)
• Global developmental delay;Microcephaly (1 variants)
• Severe combined immunodeficiency disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM2B 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				6	4	10
missense	1	1	48	4		54
nonsense			3			3
start loss						0
frameshift			2	1		3
inframe indel	1					1
splice donor/acceptor (+/-2bp)			1			1
splice region			1		1	2
non coding			1			1
Total	2	1	55	11	4

Variants in KDM2B

This is a list of pathogenic ClinVar variants found in the KDM2B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121430113-G-A		KDM2B-related disorder	Likely benign (Apr 11, 2019)
12-121430121-C-T		KDM2B-related disorder	Uncertain significance (Jan 31, 2023)
12-121430125-C-T		KDM2B-related disorder	Likely benign (Feb 04, 2020)
12-121430138-G-A		KDM2B-related disorder	Uncertain significance (Feb 05, 2024)
12-121430362-G-A			Uncertain significance (Aug 25, 2022)
12-121430436-A-G			Uncertain significance (Dec 08, 2023)
12-121439873-G-A		KDM2B-related disorder	Likely benign (Jun 07, 2019)
12-121439920-T-C		Inborn genetic diseases	Uncertain significance (Oct 18, 2021)
12-121439935-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2022)
12-121439936-G-A		KDM2B-related disorder	Benign (Feb 19, 2019)
12-121439987-G-T			Likely benign (Mar 29, 2018)
12-121440040-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
12-121440835-C-T		KDM2B-related disorder	Benign (Aug 09, 2019)
12-121440852-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
12-121440856-C-T		KDM2B-related disorder	Benign (Oct 18, 2019)
12-121440904-C-A		KDM2B-related disorder	Benign (Dec 31, 2019)
12-121440930-C-T			Uncertain significance (May 08, 2023)
12-121440956-G-A			Uncertain significance (Dec 16, 2022)
12-121440981-G-C		KDM2B-related disorder	Likely benign (Aug 09, 2019)
12-121441139-C-T			Uncertain significance (Jul 01, 2022)
12-121441213-C-G		Severe combined immunodeficiency disease	Uncertain significance (Mar 23, 2023)
12-121441216-A-G			Uncertain significance (Dec 19, 2022)
12-121442181-C-A			Uncertain significance (Feb 15, 2023)
12-121442267-G-A		KDM2B-related disorder	Benign (Dec 31, 2019)
12-121442279-C-A		KDM2B-related disorder	Likely benign (Aug 09, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM2B	protein_coding	protein_coding	ENST00000377071	23	152021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.84e-7	124787	0	7	124794	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.44	573	856	0.669	0.0000575	8701
Missense in Polyphen		125	303.21	0.41225		2996
Synonymous	0.173	353	357	0.988	0.0000252	2589
Loss of Function	6.87	6	66.4	0.0904	0.00000337	735

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000362	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that demethylates 'Lys-4' and 'Lys- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:17994099}.
• Pathway: HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.628
• rvis_EVS: -2.17
• rvis_percentile_EVS: 1.42

Haploinsufficiency Scores

• pHI: 0.382
• hipred: Y
• hipred_score: 0.756
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdm2b
• Phenotype: cellular phenotype; growth/size/body region phenotype; 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); limbs/digits/tail phenotype; vision/eye 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); reproductive system phenotype; 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); embryo phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;spermatogenesis;midbrain-hindbrain boundary morphogenesis;fourth ventricle development;lateral ventricle development;third ventricle development;initiation of neural tube closure;positive regulation of cell growth;forebrain development;midbrain development;hindbrain development;histone H2A monoubiquitination;negative regulation of neuron apoptotic process;embryonic camera-type eye morphogenesis;oxidation-reduction process;histone H3-K36 demethylation;positive regulation of stem cell population maintenance;negative regulation of neural precursor cell proliferation
• Cellular component: nucleus;nucleoplasm;nucleolus;PcG protein complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA binding;protein binding;zinc ion binding;rRNA binding;histone demethylase activity;histone demethylase activity (H3-K36 specific)