HES1
hes family bHLH transcription factor 1, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 3:194136148-194138732
Previous symbols: [ "HRY" ]
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 HES1 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 | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 1 | 0 |
Variants in HES1
This is a list of pathogenic ClinVar variants found in the HES1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-194137034-G-A | not specified | Uncertain significance (Oct 27, 2021) | ||
| 3-194137678-C-T | Benign (Jun 16, 2018) | |||
| 3-194137722-G-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 3-194137778-G-A | not specified | Uncertain significance (Nov 08, 2024) | ||
| 3-194137802-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 3-194137859-G-C | not specified | Uncertain significance (Mar 03, 2022) | ||
| 3-194137883-G-T | not specified | Uncertain significance (Dec 30, 2024) | ||
| 3-194137902-C-T | not specified | Uncertain significance (Jan 18, 2025) | ||
| 3-194137934-G-A | not specified | Uncertain significance (Nov 15, 2021) | ||
| 3-194137953-T-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 3-194137968-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 3-194137973-G-C | not specified | Uncertain significance (Sep 27, 2024) | ||
| 3-194137977-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 3-194137982-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 3-194138073-A-G | not specified | Uncertain significance (Aug 11, 2024) | ||
| 3-194138115-G-C | not specified | Uncertain significance (May 30, 2023) | ||
| 3-194138129-G-C | not specified | Uncertain significance (Jun 17, 2024) | ||
| 3-194138167-C-T | Likely benign (Jul 10, 2018) | |||
| 3-194138172-T-G | not specified | Uncertain significance (Jan 24, 2025) | ||
| 3-194138199-C-T | not specified | Uncertain significance (Dec 02, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HES1 | protein_coding | protein_coding | ENST00000232424 | 4 | 2588 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.707 | 0.290 | 125679 | 0 | 2 | 125681 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.795 | 131 | 159 | 0.823 | 0.00000715 | 1790 |
| Missense in Polyphen | 33 | 45.642 | 0.72302 | 544 | ||
| Synonymous | 0.601 | 64 | 70.4 | 0.909 | 0.00000326 | 606 |
| Loss of Function | 2.36 | 1 | 8.35 | 0.120 | 3.65e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000613 | 0.0000613 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional repressor of genes that require a bHLH protein for their transcription. May act as a negative regulator of myogenesis by inhibiting the functions of MYOD1 and ASH1. Binds DNA on N-box motifs: 5'-CACNAG-3' with high affinity and on E-box motifs: 5'-CANNTG-3' with low affinity (By similarity). May play a role in a functional FA core complex response to DNA cross-link damage, being required for the stability and nuclear localization of FA core complex proteins, as well as for FANCD2 monoubiquitination in response to DNA damage. {ECO:0000250, ECO:0000269|PubMed:18550849}.;
- Pathway
- Fanconi anemia pathway - Homo sapiens (human);Breast cancer - Homo sapiens (human);Maturity onset diabetes of the young - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Signaling by NOTCH2;Signaling by NOTCH1;Neural Crest Differentiation;Notch Signaling Pathway;Gene regulatory network modelling somitogenesis;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;miR-148a-miR-31-FIH1-HIF1α-Notch signaling in glioblastoma;Canonical and Non-canonical Notch signaling;Transcriptional regulation by RUNX3;PTF1A related regulatory pathway;Notch Signaling Pathway;Notch Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Notch;Disease;RUNX3 regulates NOTCH signaling;Signal Transduction;Gene expression (Transcription);Transcriptional regulation by RUNX3;segmentation clock;Generic Transcription Pathway;RNA Polymerase II Transcription;ATF-2 transcription factor network;Signaling by NOTCH1;NOTCH2 intracellular domain regulates transcription;Signaling by NOTCH2;NOTCH3 Intracellular Domain Regulates Transcription;Signaling by NOTCH3;Signaling by NOTCH;Fanconi anemia pathway;C-MYB transcription factor network;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;ID;Notch-mediated HES/HEY network;Diseases of signal transduction;Validated transcriptional targets of deltaNp63 isoforms;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Intolerance Scores
- loftool
- 0.0923
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.938
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.566
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hes1
- Phenotype
- cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; 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); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; neoplasm; 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; hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype;
Zebrafish Information Network
- Gene name
- her6
- Affected structure
- hindbrain
- Phenotype tag
- abnormal
- Phenotype quality
- increased occurrence
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;somitogenesis;liver development;embryonic heart tube morphogenesis;outflow tract morphogenesis;regulation of secondary heart field cardioblast proliferation;ventricular septum development;cell adhesion;Notch signaling pathway;smoothened signaling pathway;nervous system development;positive regulation of cell population proliferation;cell migration;telencephalon development;midbrain-hindbrain boundary morphogenesis;oculomotor nerve development;trochlear nerve development;hindbrain morphogenesis;forebrain radial glial cell differentiation;adenohypophysis development;cell differentiation;lung development;positive regulation of BMP signaling pathway;midbrain development;pancreas development;somatic stem cell population maintenance;ascending aorta morphogenesis;positive regulation of T cell proliferation;positive regulation of tyrosine phosphorylation of STAT protein;auditory receptor cell fate determination;positive regulation of DNA binding;regulation of fat cell differentiation;negative regulation of inner ear auditory receptor cell differentiation;positive regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of mitotic cell cycle, embryonic;lateral inhibition;regulation of JAK-STAT cascade;positive regulation of JAK-STAT cascade;cell maturation;thymus development;cell morphogenesis involved in neuron differentiation;positive regulation of astrocyte differentiation;negative regulation of oligodendrocyte differentiation;artery morphogenesis;regulation of epithelial cell proliferation;regulation of neurogenesis;inner ear receptor cell stereocilium organization;regulation of timing of neuron differentiation;negative regulation of glial cell proliferation;ventricular septum morphogenesis;ureteric bud morphogenesis;labyrinthine layer blood vessel development;common bile duct development;negative regulation of stomach neuroendocrine cell differentiation;cardiac neural crest cell development involved in outflow tract morphogenesis;pharyngeal arch artery morphogenesis;protein-containing complex assembly;glomerulus vasculature development;comma-shaped body morphogenesis;S-shaped body morphogenesis;renal interstitial fibroblast development;metanephric nephron tubule morphogenesis;cochlea development;establishment of epithelial cell polarity;vascular smooth muscle cell development;neuronal stem cell population maintenance;negative regulation of pancreatic A cell differentiation;negative regulation of stem cell differentiation;negative regulation of pro-B cell differentiation;negative regulation of forebrain neuron differentiation
- Cellular component
- nucleus;nucleoplasm;cytoplasm
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;protein homodimerization activity;histone deacetylase binding;sequence-specific DNA binding;chaperone binding;E-box binding;N-box binding;sequence-specific double-stranded DNA binding