JAZF1
Basic information
Region (hg38): 7:27830573-28180795
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the JAZF1 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in JAZF1
This is a list of pathogenic ClinVar variants found in the JAZF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-27832837-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 7-27840765-A-G | not specified | Uncertain significance (Jun 29, 2023) | ||
| 7-27840820-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 7-27895293-G-T | not specified | Uncertain significance (Apr 11, 2023) | ||
| 7-27895354-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 7-27991969-C-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 7-27991980-A-T | not specified | Uncertain significance (Dec 08, 2021) | ||
| 7-28149792-T-C | Benign (Apr 28, 2020) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| JAZF1 | protein_coding | protein_coding | ENST00000283928 | 5 | 350171 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.896 | 0.104 | 121066 | 0 | 1 | 121067 | 0.00000413 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.35 | 66 | 146 | 0.453 | 0.00000823 | 1589 |
| Missense in 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 |
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) | 0.00000905 | 0.00000905 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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
Haploinsufficiency Scores
- pHI
- 0.490
- hipred
- Y
- hipred_score
- 0.688
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Jazf1
- Phenotype
Zebrafish Information Network
- Gene name
- jazf1b
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- increased curvature
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;lipid metabolic process
- Cellular component
- fibrillar center;nucleus;cytosol;transcriptional repressor complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;transcription corepressor activity;protein binding;metal ion binding