KDM3B

lysine demethylase 3B, the group of Lysine demethylases

Basic information

Region (hg38): 5:138352685-138437028

Previous symbols: [ "C5orf7", "JMJD1B" ]

Links

ENSG00000120733 ∙ NCBI:51780 ∙ OMIM:609373 ∙ HGNC:1337 ∙ Uniprot:Q7LBC6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diets-Jongmans syndrome (Moderate), mode of inheritance: AD
• Diets-Jongmans syndrome (Strong), mode of inheritance: AD
• Diets-Jongmans syndrome (Strong), mode of inheritance: AD
• Diets-Jongmans syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diets-Jongmans syndrome	AD	Audiologic/Otolaryngologic; Oncologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Multiple patients were ascertained from a cohort of children with cancer, and a potential elevated risk of cancer may indicate that awareness may allow early diagnosis and management of oncologic sequelae	Audiologic/Otolaryngologic; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic	29351919; 30929739

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KDM3B gene.

• not provided (4 variants)
• Diets-Jongmans syndrome (2 variants)
• Neurodevelopmental disorder (1 variants)
• Rare genetic epilepsy;Rare genetic intellectual disability (1 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM3B 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			2	24	9	35
missense	3	3	117	25	6	154
nonsense	4	4				8
start loss						0
frameshift	1	2	1			4
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)		1	1			2
splice region			1	3	2	6
non coding					1	1
Total	8	11	122	49	16

Variants in KDM3B

This is a list of pathogenic ClinVar variants found in the KDM3B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-138352808-G-A		KDM3B-related disorder	Benign (Nov 01, 2019)
5-138352820-G-A		not specified	Uncertain significance (Jul 08, 2024)
5-138352825-C-G			Likely benign (Jul 01, 2024)
5-138352827-A-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
5-138352857-C-G		Inborn genetic diseases	Uncertain significance (Oct 12, 2021)
5-138352858-GGCCTCA-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 01, 2023)
5-138352864-A-AGCCTCG		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
5-138352882-C-CGCGGCGGCA		not specified	Uncertain significance (May 06, 2024)
5-138352887-C-T		not specified	Uncertain significance (Jun 27, 2023)
5-138352892-G-C		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
5-138352899-G-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
5-138352901-G-A		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
5-138352922-C-T		Inborn genetic diseases	Likely benign (Mar 17, 2023)
5-138352928-C-T		Diets-Jongmans syndrome	Pathogenic (Apr 14, 2020)
5-138352931-G-T			Uncertain significance (Jun 12, 2023)
5-138352936-G-T			Uncertain significance (Apr 22, 2023)
5-138352947-C-T		Inborn genetic diseases	Uncertain significance (Oct 22, 2024)
5-138372745-C-T		Diets-Jongmans syndrome • KDM3B-related disorder	Benign (Aug 19, 2021)
5-138372746-G-A			Uncertain significance (Oct 11, 2019)
5-138372758-G-T		Diets-Jongmans syndrome	Pathogenic (Jan 22, 2021)
5-138372783-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
5-138372792-C-T			Uncertain significance (Jan 13, 2022)
5-138372812-C-T		Neurodevelopmental disorder	Pathogenic (Jun 17, 2022)
5-138375093-A-G		KDM3B-related disorder	Uncertain significance (Jul 10, 2023)
5-138375100-C-T		Diets-Jongmans syndrome	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM3B	protein_coding	protein_coding	ENST00000314358	24	84433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.04e-12	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.98	524	958	0.547	0.0000525	11457
Missense in Polyphen		86	301.08	0.28564		3608
Synonymous	0.245	361	367	0.984	0.0000204	3620
Loss of Function	8.17	1	79.7	0.0125	0.00000481	863

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity. {ECO:0000269|PubMed:16603237}.
• Pathway: Thermogenesis - Homo sapiens (human);HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.74

Haploinsufficiency Scores

• pHI: 0.454
• hipred: Y
• hipred_score: 0.728
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdm3b

Gene ontology

• Biological process: histone H3-K9 demethylation;oxidation-reduction process;response to cisplatin;cellular oxidant detoxification
• Cellular component: chromatin;nucleus;nucleoplasm
• Molecular function: transcription regulatory region sequence-specific DNA binding;antioxidant activity;chromatin DNA binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);metal ion binding;dioxygenase activity