HES5
hes family bHLH transcription factor 5, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 1:2528745-2530263
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 HES5 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 | 2 | |||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 1 | 1 |
Variants in HES5
This is a list of pathogenic ClinVar variants found in the HES5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-2529513-C-T | not specified | Uncertain significance (Jan 27, 2025) | ||
| 1-2529521-G-T | not specified | Uncertain significance (Mar 08, 2024) | ||
| 1-2529522-C-T | not specified | Uncertain significance (Mar 08, 2024) | ||
| 1-2529525-T-C | not specified | Uncertain significance (Jan 31, 2022) | ||
| 1-2529540-G-A | not specified | Uncertain significance (Jan 01, 2025) | ||
| 1-2529639-T-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-2529653-T-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-2529659-G-A | not specified | Uncertain significance (Aug 21, 2024) | ||
| 1-2529659-G-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 1-2529688-C-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-2529719-A-G | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-2529738-C-T | not specified | Uncertain significance (Jan 19, 2025) | ||
| 1-2529851-C-T | not specified | Uncertain significance (Aug 31, 2023) | ||
| 1-2529863-T-A | not specified | Uncertain significance (Oct 12, 2024) | ||
| 1-2529877-C-T | Likely benign (Jun 05, 2018) | |||
| 1-2529926-A-C | not specified | Uncertain significance (Oct 12, 2022) | ||
| 1-2529928-C-G | not specified | Uncertain significance (May 08, 2023) | ||
| 1-2529976-G-C | not specified | Uncertain significance (Sep 19, 2022) | ||
| 1-2530132-G-A | Benign (Jun 05, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HES5 | protein_coding | protein_coding | ENST00000378453 | 3 | 1501 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.249 | 0.651 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.594 | 49 | 38.6 | 1.27 | 0.00000174 | 1038 |
| Missense in Polyphen | 25 | 21.329 | 1.1721 | 356 | ||
| Synonymous | -0.549 | 19 | 16.2 | 1.17 | 7.44e-7 | 327 |
| Loss of Function | 1.20 | 1 | 3.39 | 0.295 | 1.47e-7 | 60 |
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) | 0.00 | 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. Plays an important role as neurogenesis negative regulator (By similarity). {ECO:0000250}.;
- Pathway
- Breast cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Signaling by NOTCH2;Signaling by NOTCH1;Neural Crest Differentiation;Notch Signaling Pathway;Notch Signaling Pathway;Notch Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Disease;Signal Transduction;Signaling by NOTCH1;NOTCH2 intracellular domain regulates transcription;Signaling by NOTCH2;Signaling by NOTCH;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;Diseases of signal transduction;CDC42 signaling events;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Recessive Scores
- pRec
- 0.423
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hes5
- Phenotype
- growth/size/body region phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; cellular phenotype; craniofacial phenotype; vision/eye 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); embryo phenotype; respiratory system 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;
Zebrafish Information Network
- Gene name
- her2
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;somitogenesis;chondrocyte differentiation;cell adhesion;Notch signaling pathway;smoothened signaling pathway;brain development;positive regulation of cell population proliferation;oligodendrocyte development;telencephalon development;glial cell fate commitment;forebrain radial glial cell differentiation;neural tube development;central nervous system myelination;cell differentiation;positive regulation of BMP signaling pathway;regulation of myelination;inner ear auditory receptor cell differentiation;positive regulation of tyrosine phosphorylation of STAT protein;auditory receptor cell fate determination;camera-type eye development;regulation of cell differentiation;regulation of inner ear auditory receptor cell differentiation;negative regulation of neuron differentiation;positive regulation of Notch signaling pathway;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of JAK-STAT cascade;cell maturation;positive regulation of smooth muscle cell proliferation;astrocyte differentiation;negative regulation of astrocyte differentiation;negative regulation of oligodendrocyte differentiation;regulation of epithelial cell proliferation;regulation of neurogenesis;cartilage development;inner ear receptor cell stereocilium organization;protein-containing complex assembly;comma-shaped body morphogenesis;S-shaped body morphogenesis;specification of loop of Henle identity;metanephric nephron tubule morphogenesis;establishment of epithelial cell polarity;neuronal stem cell population maintenance;negative regulation of stem cell differentiation;negative regulation of pro-B cell differentiation;negative regulation of forebrain neuron differentiation;negative regulation of inner ear receptor cell differentiation
- Cellular component
- cellular_component;nucleus;nucleoplasm
- 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;chromatin binding;transcription corepressor activity;transcription factor binding;sequence-specific DNA binding;protein dimerization activity;sequence-specific double-stranded DNA binding