ID2
inhibitor of DNA binding 2, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 2:8678845-8684461
Links
Phenotypes
GenCC
Source:
- congenital heart disease (Disputed Evidence), mode of inheritance: AD
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 ID2 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 | 1 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 1 |
Variants in ID2
This is a list of pathogenic ClinVar variants found in the ID2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-8682176-T-C | not specified | Uncertain significance (Nov 19, 2022) | ||
| 2-8682206-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 2-8682250-G-A | not specified | Uncertain significance (Feb 08, 2023) | ||
| 2-8682268-C-T | Benign (Sep 14, 2018) | |||
| 2-8682385-G-A | not specified | Uncertain significance (Jun 07, 2024) | ||
| 2-8682409-C-A | not specified | Uncertain significance (Feb 26, 2025) | ||
| 2-8682427-C-G | not specified | Uncertain significance (Apr 07, 2023) | ||
| 2-8682442-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 2-8682446-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
| 2-8682467-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
| 2-8682473-T-G | not specified | Uncertain significance (Feb 14, 2025) | ||
| 2-8682485-A-G | not specified | Uncertain significance (May 06, 2022) | ||
| 2-8682859-C-T | not specified | Uncertain significance (Oct 27, 2021) | ||
| 2-8682880-G-A | not specified | Uncertain significance (Aug 10, 2023) | ||
| 2-8682885-G-A | not specified | Uncertain significance (Sep 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ID2 | protein_coding | protein_coding | ENST00000234091 | 2 | 5609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.669 | 0.311 | 125733 | 0 | 2 | 125735 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0175 | 73 | 73.4 | 0.994 | 0.00000326 | 892 |
| Missense in Polyphen | 15 | 22.843 | 0.65666 | 297 | ||
| Synonymous | -4.12 | 63 | 32.9 | 1.91 | 0.00000156 | 263 |
| Loss of Function | 1.76 | 0 | 3.60 | 0.00 | 1.53e-7 | 49 |
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) | 0.0000176 | 0.0000176 |
| 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. Inhibits skeletal muscle and cardiac myocyte differentiation. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Restricts the CLOCK and ARNTL/BMAL1 localization to the cytoplasm. Plays a role in both the input and output pathways of the circadian clock: in the input component, is involved in modulating the magnitude of photic entrainment and in the output component, contributes to the regulation of a variety of liver clock-controlled genes involved in lipid metabolism. {ECO:0000269|PubMed:20861012}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);miRs in Muscle Cell Differentiation;Cell Differentiation - Index expanded;miR-517 relationship with ARCN1 and USP1;Olfactory bulb development and olfactory learning;Development of pulmonary dendritic cells and macrophage subsets;Development and heterogeneity of the ILC family;EMT transition in Colorectal Cancer;ID signaling pathway;ID;Regulation of nuclear beta catenin signaling and target gene transcription;Validated targets of C-MYC transcriptional repression;Validated targets of C-MYC transcriptional activation;HIF-1-alpha transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.493
Intolerance Scores
- loftool
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.739
- hipred
- Y
- hipred_score
- 0.767
- ghis
- 0.588
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Id2
- Phenotype
- taste/olfaction phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; 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); cellular 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); neoplasm; hematopoietic system 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- id2a
- Affected structure
- retinal bipolar neuron
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;metanephros development;natural killer cell differentiation;thigmotaxis;membranous septum morphogenesis;bundle of His development;multicellular organism development;circadian rhythm;adult locomotory behavior;positive regulation of gene expression;negative regulation of gene expression;oligodendrocyte development;regulation of lipid metabolic process;olfactory bulb development;neuron differentiation;circadian regulation of gene expression;mammary gland epithelial cell proliferation;regulation of circadian rhythm;entrainment of circadian clock by photoperiod;enucleate erythrocyte differentiation;negative regulation of DNA binding;negative regulation of DNA-binding transcription factor activity;locomotor rhythm;negative regulation of B cell differentiation;positive regulation of fat cell differentiation;positive regulation of erythrocyte differentiation;positive regulation of macrophage differentiation;negative regulation of neuron differentiation;negative regulation of osteoblast differentiation;positive regulation of blood pressure;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;cell maturation;Peyer's patch development;embryonic digestive tract morphogenesis;positive regulation of smooth muscle cell proliferation;neuron fate commitment;cell morphogenesis involved in neuron differentiation;positive regulation of astrocyte differentiation;negative regulation of oligodendrocyte differentiation;regulation of cell cycle;adipose tissue development;mammary gland alveolus development;epithelial cell differentiation involved in mammary gland alveolus development;endodermal digestive tract morphogenesis;positive regulation of cell cycle arrest;cellular response to lithium ion;positive regulation of transcription involved in G1/S transition of mitotic cell cycle;cellular senescence;regulation of G1/S transition of mitotic cell cycle;negative regulation of neural precursor cell proliferation
- Cellular component
- nucleus;cytoplasm;cytosol;protein-containing complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;ion channel binding;protein dimerization activity