JAZF1
protein-codingJAZF zinc finger 1, the group of Zinc fingers C2H2-type|Tip60/Nua4 histone acetyltransferase complex subunits
Gene summary
This gene encodes a nuclear protein with three C2H2-type zinc fingers, and functions as a transcriptional repressor. Chromosomal aberrations involving this gene are associated with endometrial stromal tumors. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~350.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0007915
Submitter: Orphanet
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to JAZF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_175061.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 1 | 0 | 26 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_778231.2 | 5 | MANE Select | |
| Ensembl | ENSP00000283928.5 | 5 | MANE Select | |
| Ensembl | ENSP00000388302.1 | 4 | Standard | |
| Ensembl | ENSP00000387976.1 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| jazf1b | Danio rerio | Structure: whole organism Quality: increased curvature abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription by RNA polymerase II
- lipid metabolic process
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- nucleic acid binding
- transcription corepressor activity
- protein binding
- metal ion binding
Cellular Component
- fibrillar center
- nucleus
- cytosol
- transcriptional repressor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000283928
- Coding exons
- 5
- Length
- 350171
- Individuals with no LoFs
- 121066
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 121067
- p
- 0.00000413
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.35 | 66 | 146 | 0.453 | 0.00000823 | 1589 |
| Missense (PolyPhen) | 10 | 42.566 | 0.23493 | 494 | ||
| Synonymous | -0.896 | 68 | 59.2 | 1.15 | 0.00000355 | 473 |
| Loss of Function | 2.90 | 1 | 11.7 | 0.0853 | 6.45e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000090 | 0.0000090 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a transcriptional corepressor of orphan nuclear receptor NR2C2 (PubMed:15302918). Inhibits expression of the gluconeogenesis enzyme PCK2 through inhibition of NR2C2 activity (By similarity). Also involved in transcriptional activation of NAMPT by promoting expression of PPARA and PPARD (By similarity). Plays a role in lipid metabolism by suppressing lipogenesis, increasing lipolysis and decreasing lipid accumulation in adipose tissue (By similarity). Plays a role in glucose homeostasis by improving glucose metabolism and insulin sensitivity (By similarity). {ECO:0000250|UniProtKB:Q80ZQ5, ECO:0000269|PubMed:15302918}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.399
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |