JADE2

jade family PHD finger 2, the group of PHD finger proteins

Basic information

Region (hg38): 5:134524312-134583230

Previous symbols: [ "PHF15" ]

Links

ENSG00000043143 ∙ NCBI:23338 ∙ OMIM:610515 ∙ HGNC:22984 ∙ Uniprot:Q9NQC1 ∙ 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 JADE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JADE2 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						0
missense			29	2	1	32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	1

Variants in JADE2

This is a list of pathogenic ClinVar variants found in the JADE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134552178-G-A		not specified	Uncertain significance (Nov 05, 2021)
5-134552202-G-C		not specified	Uncertain significance (Oct 31, 2023)
5-134559913-C-T			Benign (Jun 14, 2018)
5-134559973-C-T		not specified	Uncertain significance (Jun 24, 2022)
5-134560880-G-A		not specified	Uncertain significance (May 08, 2024)
5-134566134-G-A		not specified	Likely benign (May 16, 2022)
5-134566183-G-A		not specified	Uncertain significance (Aug 18, 2023)
5-134566188-A-G		not specified	Uncertain significance (Mar 29, 2022)
5-134566352-G-T		not specified	Uncertain significance (Jan 24, 2023)
5-134566408-A-T		not specified	Uncertain significance (Sep 27, 2021)
5-134573685-C-A		not specified	Uncertain significance (Mar 03, 2022)
5-134573709-A-G		not specified	Uncertain significance (Jul 26, 2021)
5-134576856-G-GA		JADE2-associated Neurodevelopmental Disorder	Uncertain significance (Aug 06, 2021)
5-134578574-A-G		not specified	Uncertain significance (Oct 30, 2023)
5-134578619-G-A		not specified	Uncertain significance (Jun 07, 2022)
5-134578711-C-A		not specified	Uncertain significance (Aug 30, 2022)
5-134578727-C-G		not specified	Uncertain significance (Dec 06, 2022)
5-134578794-C-T		not specified	Uncertain significance (Jul 14, 2022)
5-134578796-C-T		not specified	Uncertain significance (Mar 17, 2023)
5-134578800-C-G		not specified	Uncertain significance (Apr 19, 2024)
5-134578800-C-T		not specified	Uncertain significance (May 15, 2023)
5-134578863-A-G		not specified	Uncertain significance (Jun 06, 2023)
5-134578893-G-A		not specified	Uncertain significance (Nov 03, 2023)
5-134578933-C-A		not specified	Uncertain significance (Dec 21, 2022)
5-134578961-C-T		not specified	Uncertain significance (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JADE2	protein_coding	protein_coding	ENST00000395003	10	58916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000649	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	347	502	0.691	0.0000320	5109
Missense in Polyphen		107	217.46	0.49205		2374
Synonymous	-0.113	216	214	1.01	0.0000150	1615
Loss of Function	5.26	2	36.2	0.0553	0.00000207	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000264
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the HBO1 complex which has a histone H4- specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo (PubMed:16387653). Acts as a E3 ubiquitin- protein ligase mediating the ubiquitination and subsequent proteasomal degradation of target protein histone demethylase KDM1A (PubMed:25018020). Also acts as a ubiquitin ligase E3 toward itself. Positive regulator of neurogenesis (By similarity). {ECO:0000250|UniProtKB:Q6ZQF7, ECO:0000269|PubMed:16387653}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.75

Haploinsufficiency Scores

• pHI: 0.550
• hipred: Y
• hipred_score: 0.662
• ghis: 0.552

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jade2

Gene ontology

• Biological process: protein ubiquitination;histone H3 acetylation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K12 acetylation;histone H4-K16 acetylation
• Cellular component: histone acetyltransferase complex;nucleoplasm;extracellular exosome
• Molecular function: protein binding;transferase activity;metal ion binding