ID4
inhibitor of DNA binding 4, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 6:19837370-19842197
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 ID4 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in ID4
This is a list of pathogenic ClinVar variants found in the ID4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-19837809-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 6-19837825-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 6-19837854-A-T | not specified | Uncertain significance (Feb 13, 2023) | ||
| 6-19837858-T-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 6-19837878-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
| 6-19837888-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 6-19837899-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 6-19838014-A-C | not specified | Uncertain significance (Dec 19, 2023) | ||
| 6-19838106-C-G | not specified | Uncertain significance (Jan 29, 2024) | ||
| 6-19838119-C-G | not specified | Uncertain significance (Dec 13, 2023) | ||
| 6-19838143-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 6-19838191-A-C | not specified | Uncertain significance (Aug 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ID4 | protein_coding | protein_coding | ENST00000378700 | 2 | 3299 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0312 | 0.618 | 125517 | 0 | 8 | 125525 | 0.0000319 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.855 | 77 | 58.6 | 1.31 | 0.00000261 | 989 |
| Missense in Polyphen | 18 | 19.207 | 0.93715 | 289 | ||
| Synonymous | -4.16 | 56 | 28.0 | 2.00 | 0.00000131 | 355 |
| Loss of Function | 0.233 | 2 | 2.39 | 0.837 | 1.01e-7 | 44 |
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) | 0.0000371 | 0.0000353 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000327 | 0.000327 |
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 (By similarity). {ECO:0000250}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Vitamin D Receptor Pathway;ID
(Consensus)
Recessive Scores
- pRec
- 0.194
Haploinsufficiency Scores
- pHI
- 0.277
- hipred
- Y
- hipred_score
- 0.546
- ghis
- 0.620
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.647
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Id4
- Phenotype
- reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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); endocrine/exocrine gland 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;neuroblast proliferation;circadian rhythm;positive regulation of cell population proliferation;hippocampus development;cerebral cortex neuron differentiation;central nervous system myelination;neuron differentiation;cellular protein localization;negative regulation of DNA binding;fat cell differentiation;negative regulation of fat cell differentiation;negative regulation of neuron differentiation;positive regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of astrocyte differentiation;negative regulation of oligodendrocyte differentiation;regulation of cell cycle;prostate gland epithelium morphogenesis;prostate gland stromal morphogenesis;seminal vesicle morphogenesis
- 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 dimerization activity