HES2
Basic information
Region (hg38): 1:6412418-6424670
Links
Phenotypes
GenCC
Source:
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 HES2 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 | 18 | 18 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 0 | 0 | 18 | 0 | 2 |
Variants in HES2
This is a list of pathogenic ClinVar variants found in the HES2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-6418923-G-C | not specified | Uncertain significance (Feb 28, 2024) | ||
1-6418928-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
1-6418938-C-A | not specified | Uncertain significance (Jun 29, 2022) | ||
1-6418979-G-C | not specified | Uncertain significance (Aug 03, 2022) | ||
1-6418992-C-T | not specified | Uncertain significance (Jul 27, 2022) | ||
1-6419067-C-T | not specified | Uncertain significance (May 24, 2024) | ||
1-6419102-G-A | not specified | Uncertain significance (Oct 05, 2022) | ||
1-6419117-C-A | not specified | Uncertain significance (Jun 24, 2022) | ||
1-6419123-C-G | not specified | Uncertain significance (Jun 13, 2024) | ||
1-6419127-A-G | not specified | Uncertain significance (Sep 29, 2022) | ||
1-6419247-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
1-6419264-G-A | not specified | Uncertain significance (Feb 02, 2022) | ||
1-6419327-G-A | not specified | Uncertain significance (Dec 04, 2024) | ||
1-6419333-T-C | not specified | Uncertain significance (Aug 03, 2022) | ||
1-6419656-T-C | not specified | Uncertain significance (Jan 26, 2023) | ||
1-6419690-G-T | not specified | Uncertain significance (Oct 20, 2024) | ||
1-6419701-C-T | not specified | Uncertain significance (Oct 20, 2023) | ||
1-6419808-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
1-6424615-C-A | Benign (Nov 29, 2018) | |||
1-6424625-G-A | Benign (Nov 29, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HES2 | protein_coding | protein_coding | ENST00000377834 | 4 | 12253 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00263 | 0.576 | 122717 | 0 | 5 | 122722 | 0.0000204 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.838 | 43 | 61.5 | 0.699 | 0.00000291 | 1029 |
Missense in Polyphen | 18 | 24.256 | 0.74209 | 339 | ||
Synonymous | 0.999 | 24 | 31.1 | 0.772 | 0.00000148 | 409 |
Loss of Function | 0.332 | 4 | 4.78 | 0.836 | 2.11e-7 | 61 |
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) | 0.0000185 | 0.0000181 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000100 | 0.0000989 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional repressor of genes that require a bHLH protein for their transcription. {ECO:0000250}.;
- Pathway
- Human papillomavirus infection - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.109
Haploinsufficiency Scores
- pHI
- 0.510
- hipred
- N
- hipred_score
- 0.285
- ghis
- 0.605
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hes2
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;somitogenesis;Notch signaling pathway;cell differentiation;regulation of neurogenesis
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;transcription corepressor activity;transcription factor binding;sequence-specific DNA binding;protein dimerization activity;sequence-specific double-stranded DNA binding