KDM4C

lysine demethylase 4C, the group of Tudor domain containing|Lysine demethylases

Basic information

Region (hg38): 9:6720862-7175648

Previous symbols: [ "JMJD2C" ]

Links

ENSG00000107077 ∙ NCBI:23081 ∙ OMIM:605469 ∙ HGNC:17071 ∙ Uniprot:Q9H3R0 ∙ 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 KDM4C gene.

• Inborn genetic diseases (42 variants)
• not provided (8 variants)
• Enchondromatosis (2 variants)
• KDM4C-related condition (1 variants)
• Maffucci syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM4C 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	5	7
missense			45		1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	46	2	6

Variants in KDM4C

This is a list of pathogenic ClinVar variants found in the KDM4C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-6720948-G-C		KDM4C-related disorder	Uncertain significance (Sep 14, 2023)
9-6720959-A-G		Enchondromatosis	Uncertain significance (-)
9-6793056-T-C		not specified	Uncertain significance (Aug 04, 2023)
9-6793115-C-T		not specified	Uncertain significance (Aug 23, 2021)
9-6805685-C-T			Likely benign (May 01, 2022)
9-6814685-G-T		not specified	Uncertain significance (Dec 19, 2023)
9-6814707-A-G		not specified	Uncertain significance (Oct 06, 2021)
9-6849508-G-T		not specified	Uncertain significance (Nov 18, 2022)
9-6849518-A-G			Benign (Apr 30, 2018)
9-6849579-A-G		not specified	Uncertain significance (Oct 20, 2023)
9-6849650-C-T			Likely benign (Jul 01, 2022)
9-6849689-G-C			Benign (Apr 30, 2018)
9-6880058-C-G		not specified	Uncertain significance (Sep 25, 2023)
9-6887978-C-G		not specified	Uncertain significance (Oct 26, 2021)
9-6888029-C-T		not specified	Uncertain significance (May 31, 2023)
9-6888034-T-C			Benign (Apr 20, 2018)
9-6980958-A-G		not specified	Uncertain significance (Dec 15, 2023)
9-6980985-C-T		not specified	Uncertain significance (Jan 17, 2023)
9-6981021-A-G		not specified	Uncertain significance (Feb 15, 2023)
9-6981070-T-A		not specified	Uncertain significance (Dec 03, 2021)
9-6981115-G-A		Maffucci syndrome • KDM4C-related disorder	Conflicting classifications of pathogenicity (Apr 15, 2022)
9-6984189-C-G		not specified	Uncertain significance (May 09, 2023)
9-6984275-G-A		not specified	Uncertain significance (Aug 04, 2023)
9-6984303-C-T		not specified	Uncertain significance (Jul 05, 2023)
9-6984375-A-G		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM4C	protein_coding	protein_coding	ENST00000381309	21	454786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.52e-7	1.00	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.489	622	589	1.06	0.0000310	6985
Missense in Polyphen		138	195.38	0.70633		2277
Synonymous	-2.39	262	217	1.21	0.0000125	1908
Loss of Function	4.34	21	56.1	0.375	0.00000282	704

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.0000660	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:28262558}.
• Pathway: Signal Transduction;HDMs demethylate histones;Chromatin modifying enzymes;AndrogenReceptor;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;RHO GTPase Effectors;Signaling by Rho GTPases;Coregulation of Androgen receptor activity;Chromatin organization (Consensus)

Intolerance Scores

• loftool: 0.689
• rvis_EVS: -0.34
• rvis_percentile_EVS: 29.62

Haploinsufficiency Scores

• pHI: 0.707
• hipred: N
• hipred_score: 0.414
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Kdm4c
• Phenotype: immune system phenotype; hematopoietic 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); neoplasm; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blastocyst formation;chromatin remodeling;regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;positive regulation of gene expression;histone H3-K9 demethylation;positive regulation of neuron differentiation;oxidation-reduction process;histone H3-K36 demethylation;negative regulation of histone H3-K9 trimethylation;regulation of stem cell population maintenance;regulation of stem cell differentiation
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;pericentric heterochromatin;histone methyltransferase complex
• Molecular function: zinc ion binding;enzyme binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);androgen receptor binding;histone demethylase activity (H3-K36 specific)