JDP2

Jun dimerization protein 2, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 14:75427716-75474111

Previous symbols: [ "JUNDM2" ]

Links

ENSG00000140044

∙ NCBI:122953 ∙ OMIM:608657 ∙ HGNC:17546 ∙ Uniprot:Q8WYK2 ∙ 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 JDP2 gene.

not_specified (27 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_001135048.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			24 clinvar			24
nonsense						0
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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