ID3
inhibitor of DNA binding 3, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 1:23557925-23559501
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 ID3 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in ID3
This is a list of pathogenic ClinVar variants found in the ID3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-23559155-G-A | not specified | Uncertain significance (Dec 07, 2023) | ||
| 1-23559213-G-A | Neoplasm | - (-) | ||
| 1-23559282-A-T | Hereditary breast ovarian cancer syndrome | Uncertain significance (Aug 01, 2020) | ||
| 1-23559300-C-T | not specified | Uncertain significance (Jul 05, 2022) | ||
| 1-23559351-G-A | not specified | Uncertain significance (Jun 21, 2023) | ||
| 1-23559354-C-T | not specified | Uncertain significance (Mar 31, 2024) | ||
| 1-23559405-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
| 1-23559411-G-A | not specified | Uncertain significance (Jul 11, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ID3 | protein_coding | protein_coding | ENST00000374561 | 2 | 1877 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.722 | 0.266 | 125647 | 0 | 5 | 125652 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.02 | 92 | 68.2 | 1.35 | 0.00000312 | 746 |
| Missense in Polyphen | 24 | 24.514 | 0.97904 | 289 | ||
| Synonymous | -3.79 | 60 | 32.5 | 1.84 | 0.00000153 | 264 |
| Loss of Function | 1.90 | 0 | 4.22 | 0.00 | 1.84e-7 | 45 |
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) | 0.0000442 | 0.0000440 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. Implicated in regulating a variety of cellular processes, including cellular growth, senescence, differentiation, apoptosis, angiogenesis, and neoplastic transformation. Involved in myogenesis by inhibiting skeletal muscle and cardiac myocyte differentiation and promoting muscle precursor cells proliferation. Inhibits the binding of E2A-containing protein complexes to muscle creatine kinase E-box enhancer. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. {ECO:0000269|PubMed:8437843}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Adipogenesis;ID signaling pathway;ID
(Consensus)
Recessive Scores
- pRec
- 0.308
Intolerance Scores
- loftool
- 0.184
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.73
Haploinsufficiency Scores
- pHI
- 0.916
- hipred
- Y
- hipred_score
- 0.629
- ghis
- 0.418
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Id3
- Phenotype
- immune system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal 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); neoplasm; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- id3
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;metanephros development;regulation of DNA replication;transcription, DNA-templated;multicellular organism development;central nervous system development;heart development;muscle organ development;circadian rhythm;response to wounding;neuron differentiation;epithelial cell differentiation;notochord development;odontogenesis;positive regulation of apoptotic process;negative regulation of DNA binding;negative regulation of DNA-binding transcription factor activity;negative regulation of myoblast differentiation;negative regulation of neuron differentiation;negative regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;regulation of cell cycle;cellular response to leptomycin B
- Cellular component
- nucleus;cytoplasm
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;protein domain specific binding;protein dimerization activity;leptomycin B binding