ID1
inhibitor of DNA binding 1, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 20:31573014-31606515
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 ID1 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 | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 20 | 0 | 0 |
Variants in ID1
This is a list of pathogenic ClinVar variants found in the ID1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-31605402-T-G | not specified | Uncertain significance (Mar 14, 2023) | ||
| 20-31605428-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 20-31605448-G-C | not specified | Uncertain significance (Aug 16, 2021) | ||
| 20-31605467-G-T | not specified | Uncertain significance (Nov 29, 2023) | ||
| 20-31605491-T-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 20-31605494-C-A | not specified | Uncertain significance (Apr 12, 2024) | ||
| 20-31605498-G-C | not specified | Uncertain significance (Oct 21, 2024) | ||
| 20-31605533-C-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 20-31605560-A-G | not specified | Uncertain significance (Aug 13, 2021) | ||
| 20-31605597-C-T | Likely benign (Feb 01, 2025) | |||
| 20-31605604-T-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 20-31605649-A-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| 20-31605689-A-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 20-31605722-A-C | not specified | Uncertain significance (Jul 14, 2024) | ||
| 20-31605730-G-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| 20-31605745-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
| 20-31605746-G-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 20-31605754-C-G | not specified | Uncertain significance (Feb 10, 2022) | ||
| 20-31605806-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 20-31606071-G-A | not specified | Uncertain significance (Dec 09, 2023) | ||
| 20-31606086-T-C | not specified | Uncertain significance (Dec 30, 2024) | ||
| 20-31606089-C-G | not specified | Uncertain significance (Feb 22, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ID1 | protein_coding | protein_coding | ENST00000376112 | 2 | 1233 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000310 | 0.371 | 125668 | 0 | 18 | 125686 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -2.01 | 148 | 93.4 | 1.59 | 0.00000417 | 961 |
| Missense in Polyphen | 42 | 36.372 | 1.1547 | 391 | ||
| Synonymous | -3.93 | 75 | 42.4 | 1.77 | 0.00000198 | 337 |
| Loss of Function | -0.150 | 5 | 4.65 | 1.07 | 2.03e-7 | 50 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000138 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000489 | 0.0000462 |
| European (Non-Finnish) | 0.000130 | 0.000123 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| 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 (By similarity). {ECO:0000250}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Neural Crest Differentiation;Vitamin D Receptor Pathway;miR-517 relationship with ARCN1 and USP1;TGF-B Signaling in Thyroid Cells for Epithelial-Mesenchymal Transition;Hfe effect on hepcidin production;EMT transition in Colorectal Cancer;ID signaling pathway;Oncogene Induced Senescence;Cellular Senescence;Cellular responses to stress;Cellular responses to external stimuli;ID;Notch-mediated HES/HEY network;ALK1 signaling events;IL3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.656
Intolerance Scores
- loftool
- 0.341
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.510
- hipred
- Y
- hipred_score
- 0.683
- ghis
- 0.539
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Id1
- Phenotype
- respiratory system phenotype; embryo phenotype; neoplasm; 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); 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); vision/eye 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); skeleton phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- id1
- Affected structure
- brain
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;angiogenesis;endothelial cell morphogenesis;transcription, DNA-templated;transforming growth factor beta receptor signaling pathway;brain development;heart development;circadian rhythm;negative regulation of transcription by transcription factor localization;positive regulation of gene expression;neuron differentiation;BMP signaling pathway;protein destabilization;positive regulation of actin filament bundle assembly;collagen metabolic process;cell-abiotic substrate adhesion;negative regulation of apoptotic process;negative regulation of DNA binding;regulation of MAPK cascade;negative regulation of DNA-binding transcription factor activity;blood vessel endothelial cell migration;negative regulation of endothelial cell differentiation;negative regulation of neuron differentiation;negative regulation of osteoblast differentiation;regulation of angiogenesis;negative regulation of transcription, DNA-templated;response to antibiotic;blood vessel morphogenesis;positive regulation of epithelial cell proliferation;negative regulation of dendrite morphogenesis;regulation of cell cycle;lung morphogenesis;lung vasculature development;cellular response to epidermal growth factor stimulus;negative regulation of protein homodimerization activity;negative regulation of cold-induced thermogenesis;cellular response to peptide;cellular response to dopamine;cellular response to nerve growth factor stimulus
- Cellular component
- nucleus;nucleoplasm;cytoplasm;Golgi apparatus;centrosome
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription factor activity;protein binding;protein C-terminus binding;transcription factor binding;protein homodimerization activity;protein self-association;protein N-terminus binding;proteasome binding