JADE3

jade family PHD finger 3, the group of PHD finger proteins

Basic information

Region (hg38): X:46912275-47061242

Previous symbols: [ "PHF16" ]

Links

ENSG00000102221 ∙ NCBI:9767 ∙ OMIM:300618 ∙ HGNC:22982 ∙ Uniprot:Q92613 ∙ 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 JADE3 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JADE3 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				1		1
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in JADE3

This is a list of pathogenic ClinVar variants found in the JADE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-46985745-T-C		not specified	Uncertain significance (May 18, 2022)
X-46985760-A-G		not specified	Uncertain significance (Jan 09, 2024)
X-46998256-C-T		not specified	Uncertain significance (May 18, 2023)
X-47024740-G-T		not specified	Uncertain significance (Jan 04, 2024)
X-47024894-A-G		not specified	Uncertain significance (Dec 27, 2022)
X-47039049-C-T		not specified	Uncertain significance (Mar 01, 2024)
X-47054387-G-A		not specified	Uncertain significance (Jan 22, 2024)
X-47054420-G-A		not specified	Uncertain significance (Oct 26, 2022)
X-47054513-A-G		not specified	Uncertain significance (Jul 25, 2023)
X-47054567-A-T		not specified	Uncertain significance (Feb 27, 2023)
X-47054569-G-A		not specified	Uncertain significance (Aug 10, 2021)
X-47054576-G-A		not specified	Uncertain significance (Dec 16, 2023)
X-47054605-C-A		not specified	Uncertain significance (Jun 02, 2023)
X-47054611-C-T		not specified	Uncertain significance (Jun 16, 2023)
X-47056160-G-A		not specified	Uncertain significance (Sep 06, 2022)
X-47058341-T-C		not specified	Uncertain significance (Jul 12, 2022)
X-47058415-C-A		not specified	Uncertain significance (May 26, 2022)
X-47058416-G-A		not specified	Uncertain significance (Jun 11, 2021)
X-47058454-A-G		not specified	Uncertain significance (Dec 17, 2023)
X-47058457-G-C		not specified	Uncertain significance (Jun 16, 2023)
X-47058488-C-T		not specified	Uncertain significance (Mar 04, 2024)
X-47058546-T-G		not specified	Uncertain significance (Jul 06, 2022)
X-47058559-A-G		not specified	Uncertain significance (Feb 12, 2024)
X-47058680-C-G		not specified	Uncertain significance (Dec 08, 2023)
X-47058684-G-A		not specified	Likely benign (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JADE3	protein_coding	protein_coding	ENST00000218343	10	148931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000224	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	218	312	0.698	0.0000237	5506
Missense in Polyphen		34	115.61	0.2941		2113
Synonymous	0.613	108	116	0.928	0.00000891	1501
Loss of Function	4.54	0	24.0	0.00	0.00000188	437

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
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. {ECO:0000269|PubMed:16387653}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.419
• hipred: Y
• hipred_score: 0.591
• ghis: 0.484

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: Jade3
• Phenotype: normal phenotype

Gene ontology

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