KDM3A

lysine demethylase 3A, the group of Lysine demethylases

Basic information

Region (hg38): 2:86440647-86492716

Previous symbols: [ "JMJD1", "JMJD1A" ]

Links

ENSG00000115548 ∙ NCBI:55818 ∙ OMIM:611512 ∙ HGNC:20815 ∙ Uniprot:Q9Y4C1 ∙ 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 KDM3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM3A 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				7	9	16
missense			51	5	3	59
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	2	5
non coding				1	1	2
Total	0	0	52	13	13

Variants in KDM3A

This is a list of pathogenic ClinVar variants found in the KDM3A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86442060-C-G		not specified	Uncertain significance (Oct 04, 2022)
2-86442123-A-G		not specified	Uncertain significance (Sep 06, 2022)
2-86442156-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-86449809-G-T		KDM3A-related disorder	Likely benign (May 18, 2018)
2-86449895-A-G		KDM3A-related disorder	Likely benign (Mar 21, 2019)
2-86449910-C-T		not specified	Uncertain significance (Oct 20, 2023)
2-86449916-G-A		not specified	Uncertain significance (Mar 31, 2022)
2-86449924-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-86449940-G-A		not specified	Uncertain significance (Dec 06, 2021)
2-86451104-C-T		not specified	Likely benign (Dec 26, 2023)
2-86451110-A-G		not specified	Uncertain significance (Dec 19, 2022)
2-86451142-A-G		not specified	Uncertain significance (May 29, 2024)
2-86451218-A-G			Likely benign (Jun 12, 2018)
2-86455087-T-C		KDM3A-related disorder	Likely benign (Feb 22, 2019)
2-86455124-A-C		not specified	Uncertain significance (Aug 12, 2021)
2-86455154-G-T		not specified	Uncertain significance (Oct 10, 2023)
2-86456416-ATT-A		KDM3A-related disorder	Benign (Mar 26, 2019)
2-86456416-A-ATTT		KDM3A-related disorder	Benign (Nov 25, 2019)
2-86456442-G-T		not specified	Uncertain significance (May 12, 2024)
2-86456558-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-86456886-T-C		KDM3A-related disorder	Likely benign (Mar 04, 2019)
2-86457017-G-A		KDM3A-related disorder	Likely benign (Sep 19, 2019)
2-86464092-A-G		not specified	Uncertain significance (Jan 17, 2024)
2-86464130-A-G		KDM3A-related disorder	Likely benign (Jul 15, 2019)
2-86464204-A-G		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM3A	protein_coding	protein_coding	ENST00000409556	25	52070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000112	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	573	695	0.824	0.0000351	8677
Missense in Polyphen		215	339.83	0.63268		4131
Synonymous	-2.16	294	251	1.17	0.0000129	2500
Loss of Function	6.86	9	71.7	0.125	0.00000398	841

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000220	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' of histone H3, thereby playing a central role in histone code. Preferentially demethylates mono- and dimethylated H3 'Lys-9' residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 'Lys-9'. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 'Lys-9' demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1. {ECO:0000269|PubMed:16603237, ECO:0000269|PubMed:28262558}.
• Pathway: Thermogenesis - Homo sapiens (human);HDMs demethylate histones;Chromatin modifying enzymes;AndrogenReceptor;Coregulation of Androgen receptor activity;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.24

Haploinsufficiency Scores

• pHI: 0.383
• hipred: Y
• hipred_score: 0.528
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdm3a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; reproductive system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: spermatid nucleus elongation;hormone-mediated signaling pathway;androgen receptor signaling pathway;histone H3-K9 demethylation;histone H3-K9 dimethylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;formaldehyde biosynthetic process;negative regulation of histone H3-K9 methylation;oxidation-reduction process;positive regulation of cold-induced thermogenesis;cellular response to leukemia inhibitory factor;regulation of stem cell population maintenance;regulation of stem cell differentiation
• Cellular component: chromatin;nucleus;nucleoplasm;cytoplasm;membrane
• Molecular function: transcription regulatory region sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity;iron ion binding;protein binding;chromatin DNA binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);androgen receptor binding;dioxygenase activity