JADE1

jade family PHD finger 1, the group of PHD finger proteins

Basic information

Region (hg38): 4:128809699-128875224

Previous symbols: [ "PHF17" ]

Links

ENSG00000077684 ∙ NCBI:79960 ∙ OMIM:610514 ∙ HGNC:30027 ∙ Uniprot:Q6IE81 ∙ 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 JADE1 gene.

• Inborn genetic diseases (24 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JADE1 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	2
missense			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	24	0	3

Variants in JADE1

This is a list of pathogenic ClinVar variants found in the JADE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-128831772-G-T		not specified	Uncertain significance (Jun 17, 2022)
4-128843004-C-T		not specified	Uncertain significance (Nov 02, 2023)
4-128843016-A-T		not specified	Uncertain significance (Oct 04, 2022)
4-128849016-G-T		not specified	Uncertain significance (Feb 05, 2024)
4-128849025-G-C		not specified	Uncertain significance (Oct 13, 2021)
4-128849027-A-G		not specified	Uncertain significance (Dec 28, 2022)
4-128849102-G-A		not specified	Uncertain significance (Jan 26, 2022)
4-128857355-A-G			Benign (Jun 27, 2018)
4-128857397-C-A		not specified	Uncertain significance (Jan 26, 2023)
4-128861698-T-C			Benign (Feb 25, 2018)
4-128861842-C-A		not specified	Uncertain significance (Apr 04, 2023)
4-128861877-G-T		not specified	Uncertain significance (Aug 17, 2022)
4-128861879-A-G		not specified	Uncertain significance (Feb 08, 2023)
4-128861897-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-128862149-A-G		not specified	Uncertain significance (Dec 28, 2022)
4-128862172-G-A		not specified	Uncertain significance (Dec 27, 2023)
4-128867901-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-128871384-C-A		not specified	Uncertain significance (Feb 28, 2023)
4-128871517-A-G		not specified	Uncertain significance (Aug 09, 2021)
4-128871522-C-G		not specified	Uncertain significance (Jun 24, 2022)
4-128871523-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-128871632-A-G			Benign (Jun 27, 2018)
4-128871702-G-A		not specified	Uncertain significance (Jan 04, 2022)
4-128871718-A-G			Benign (Jun 27, 2018)
4-128871735-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JADE1	protein_coding	protein_coding	ENST00000226319	10	65601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00115	125735	0	9	125744	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.18	281	476	0.590	0.0000264	5566
Missense in Polyphen		27	135.04	0.19995		1501
Synonymous	1.03	167	185	0.903	0.0000100	1606
Loss of Function	5.05	4	37.3	0.107	0.00000201	442

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)	0.0000705	0.0000703
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. Transcriptional coactivator, it may also promote acetylation of nucleosomal histone H4 by KAT5. Promotes apoptosis. May act as a renal tumor suppressor. Negatively regulates canonical Wnt signaling; at least in part, cooperates with NPHP4 in this function. {ECO:0000269|PubMed:15502158, ECO:0000269|PubMed:16046545, ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:22654112}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.823
• hipred: Y
• hipred_score: 0.775
• ghis: 0.517

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: Jade1
• 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)

Zebrafish Information Network

• Gene name: jade1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased curvature

Gene ontology

• Biological process: apoptotic process;negative regulation of cell growth;histone H3 acetylation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K12 acetylation;histone H4-K16 acetylation;negative regulation of canonical Wnt signaling pathway;positive regulation of nucleic acid-templated transcription;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: histone acetyltransferase complex;nucleus;nucleoplasm;cytoplasm;plasma membrane;nuclear speck;ciliary basal body
• Molecular function: transcription coactivator activity;protein binding;metal ion binding