JARID2

jumonji and AT-rich interaction domain containing 2, the group of AT-rich interaction domain containing|Iron (II) and 2-oxoglutarate dependent oxygenases

Basic information

Region (hg38): 6:15246068-15522042

Previous symbols: [ "JMJ" ]

Links

ENSG00000008083 ∙ NCBI:3720 ∙ OMIM:601594 ∙ HGNC:6196 ∙ Uniprot:Q92833 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• syndromic intellectual disability (Supportive), mode of inheritance: AD
• developmental delay with variable intellectual disability and dysmorphic facies (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental delay with variable intellecutal disability and dysmorphic facies	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	33077894; 35533077; 35887345

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JARID2 gene.

• Inborn genetic diseases (58 variants)
• not provided (53 variants)
• JARID2-related condition (6 variants)
• Developmental delay with variable intellectual disability and dysmorphic facies (5 variants)
• Neurodevelopmental disorder (3 variants)
• JARID2-associated Neurodevelopmental disorder (2 variants)
• not specified (1 variants)
• Intellectual disability, mild (1 variants)
• Autism;Speech apraxia;Intellectual disability;Stereotypic movement disorder (1 variants)
• JARID2-related Neurodevelopmental syndrome (1 variants)
• Autosomal dominant non-syndromic intellectual disability (1 variants)
• JARID2-related Neurodevelopmental Disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JARID2 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	11	18
missense		1	71	15	4	91
nonsense			2			2
start loss						0
frameshift	5	2	1			8
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region		1	1	3		5
non coding						0
Total	5	5	74	22	15

Variants in JARID2

This is a list of pathogenic ClinVar variants found in the JARID2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-15246549-GAA-G		Autosomal dominant non-syndromic intellectual disability	Likely pathogenic (Feb 10, 2022)
6-15246570-A-C		Inborn genetic diseases	Uncertain significance (May 18, 2023)
6-15246574-A-C		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
6-15374124-G-A		JARID2-related disorder	Uncertain significance (Oct 28, 2022)
6-15374141-T-A			Uncertain significance (Dec 19, 2022)
6-15374229-C-T		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
6-15374244-CTG-C		Neurodevelopmental disorder	Pathogenic (Apr 02, 2021)
6-15410322-G-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
6-15410332-C-T			Uncertain significance (May 09, 2023)
6-15452030-G-T		Speech apraxia;Autism;Stereotypic movement disorder;Intellectual disability	Likely pathogenic (Jan 29, 2021)
6-15452072-A-G		JARID2-related disorder	Benign (Jul 11, 2019)
6-15452075-G-C		JARID2-related disorder	Uncertain significance (Sep 13, 2023)
6-15452093-AC-A		Inborn genetic diseases	Pathogenic (Sep 09, 2021)
6-15452098-C-G			Uncertain significance (Jul 01, 2023)
6-15452120-C-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
6-15452127-A-C		JARID2-related disorder	Uncertain significance (Jan 25, 2024)
6-15452170-T-C		JARID2-related disorder	Uncertain significance (Sep 01, 2023)
6-15468547-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
6-15468593-A-G		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
6-15468604-G-C			Uncertain significance (Sep 17, 2021)
6-15468627-A-G			Benign (Dec 31, 2019)
6-15468630-C-T			Likely benign (Mar 06, 2018)
6-15468645-C-G		JARID2-related disorder	Benign (Jul 15, 2021)
6-15468645-C-T			Benign/Likely benign (Jun 01, 2022)
6-15468697-A-G			Uncertain significance (Feb 24, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JARID2	protein_coding	protein_coding	ENST00000341776	18	275726

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000562	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	575	787	0.731	0.0000510	8125
Missense in Polyphen		117	243.77	0.47996		2466
Synonymous	-2.12	383	334	1.15	0.0000241	2482
Loss of Function	6.31	5	55.9	0.0894	0.00000291	654

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000328	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of histone methyltransferase complexes that plays an essential role in embryonic development, including heart and liver development, neural tube fusion process and hematopoiesis. Acts by modulating histone methyltransferase activity and promoting the recruitment of histone methyltransferase complexes to their target genes. Binds DNA and mediates the recruitment of the PRC2 complex to target genes in embryonic stem cells. Does not have histone demethylase activity but regulates activity of various histone methyltransferase complexes. In embryonic stem cells, it associates with the PRC2 complex and inhibits trimethylation of 'Lys-27' of histone H3 (H3K27me3) by the PRC2 complex, thereby playing a key role in differentiation of embryonic stem cells and normal development. In cardiac cells, it is required to repress expression of cyclin-D1 (CCND1) by activating methylation of 'Lys-9' of histone H3 (H3K9me) by the GLP1/EHMT1 and G9a/EHMT2 histone methyltransferases. Also acts as a transcriptional repressor of ANF via its interaction with GATA4 and NKX2-5. Participates in the negative regulation of cell proliferation signaling. {ECO:0000269|PubMed:20075857}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Endoderm Differentiation;Mesodermal Commitment Pathway;Interactome of polycomb repressive complex 2 (PRC2);Epigenetic regulation of gene expression;Gene expression (Transcription);PRC2 methylates histones and DNA (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.0413
• rvis_EVS: -1.74
• rvis_percentile_EVS: 2.42

Haploinsufficiency Scores

• pHI: 0.983
• hipred: Y
• hipred_score: 0.825
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jarid2
• Phenotype: normal 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); 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); hematopoietic system phenotype; embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; skeleton 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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;liver development;chromatin remodeling;central nervous system development;negative regulation of cardiac muscle hypertrophy;histone demethylation;negative regulation of histone methylation;negative regulation of gene expression, epigenetic;negative regulation of transcription, DNA-templated;spleen development;thymus development;stem cell differentiation;positive regulation of histone H3-K9 methylation;negative regulation of cardiac muscle cell proliferation;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;nucleoplasm;mitochondrion;histone methyltransferase complex;ESC/E(Z) complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;transcription factor binding;histone demethylase activity;histone demethylase activity (H3-trimethyl-K4 specific)