JDP2
Jun dimerization protein 2, the group of Basic leucine zipper proteins
Basic information
Region (hg38): 14:75427716-75474111
Previous symbols: [ "JUNDM2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 JDP2 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 | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 1 | 0 |
Variants in JDP2
This is a list of pathogenic ClinVar variants found in the JDP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-75432330-G-A | not specified | Likely benign (Sep 12, 2023) | ||
| 14-75437922-T-C | not specified | Uncertain significance (Jun 06, 2022) | ||
| 14-75437933-C-A | not specified | Uncertain significance (Jun 22, 2023) | ||
| 14-75438003-C-T | not specified | Uncertain significance (Jun 30, 2022) | ||
| 14-75438032-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 14-75438050-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 14-75438056-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 14-75438092-G-A | not specified | Uncertain significance (May 08, 2023) | ||
| 14-75438110-G-T | not specified | Uncertain significance (Mar 13, 2023) | ||
| 14-75438114-A-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 14-75461460-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 14-75461477-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 14-75461514-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
| 14-75461528-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 14-75469317-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 14-75469357-G-A | not specified | Uncertain significance (Nov 15, 2023) | ||
| 14-75469423-A-G | not specified | Uncertain significance (Mar 29, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| JDP2 | protein_coding | protein_coding | ENST00000267569 | 4 | 46396 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.359 | 0.630 | 125674 | 0 | 3 | 125677 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.923 | 83 | 110 | 0.753 | 0.00000737 | 1091 |
| Missense in Polyphen | 15 | 22.902 | 0.65497 | 264 | ||
| Synonymous | -0.00913 | 50 | 49.9 | 1.00 | 0.00000344 | 362 |
| Loss of Function | 2.14 | 2 | 8.87 | 0.226 | 6.33e-7 | 82 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000182 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the AP-1 transcription factor that represses transactivation mediated by the Jun family of proteins. Involved in a variety of transcriptional responses associated with AP-1 such as UV-induced apoptosis, cell differentiation, tumorigenesis and antitumogeneris. Can also function as a repressor by recruiting histone deacetylase 3/HDAC3 to the promoter region of JUN. May control transcription via direct regulation of the modification of histones and the assembly of chromatin. {ECO:0000269|PubMed:12707301, ECO:0000269|PubMed:12903123, ECO:0000269|PubMed:16026868, ECO:0000269|PubMed:16518400}.;
- Pathway
- Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;ATF-2 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.103
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.960
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Jdp2
- Phenotype
- skeleton phenotype; immune system phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; normal phenotype; homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of histone deacetylation;negative regulation of fat cell differentiation
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;protein binding;protein heterodimerization activity