HES2

hes family bHLH transcription factor 2, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:6412418-6424670

Links

ENSG00000069812NCBI:54626OMIM:609970HGNC:16005Uniprot:Q9Y543AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HES2 gene.

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
clinvar
18
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
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)3105492
1-6418928-G-A not specified Uncertain significance (Nov 18, 2022)2327287
1-6418938-C-A not specified Uncertain significance (Jun 29, 2022)2298832
1-6418979-G-C not specified Uncertain significance (Aug 03, 2022)2305191
1-6418992-C-T not specified Uncertain significance (Jul 27, 2022)2229349
1-6419067-C-T not specified Uncertain significance (May 24, 2024)2342352
1-6419102-G-A not specified Uncertain significance (Oct 05, 2022)2317147
1-6419117-C-A not specified Uncertain significance (Jun 24, 2022)2297522
1-6419123-C-G not specified Uncertain significance (Jun 13, 2024)3284128
1-6419127-A-G not specified Uncertain significance (Sep 29, 2022)2314770
1-6419247-C-T not specified Uncertain significance (Dec 20, 2023)3105491
1-6419264-G-A not specified Uncertain significance (Feb 02, 2022)2371019
1-6419327-G-A not specified Uncertain significance (Dec 04, 2024)3525267
1-6419333-T-C not specified Uncertain significance (Aug 03, 2022)2397490
1-6419656-T-C not specified Uncertain significance (Jan 26, 2023)2479248
1-6419690-G-T not specified Uncertain significance (Oct 20, 2024)3525266
1-6419701-C-T not specified Uncertain significance (Oct 20, 2023)3105493
1-6419808-G-A not specified Uncertain significance (Aug 10, 2021)2242294
1-6424615-C-A Benign (Nov 29, 2018)1296853
1-6424625-G-A Benign (Nov 29, 2018)1231326

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HES2protein_codingprotein_codingENST00000377834 412253
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002630.576122717051227220.0000204
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8384361.50.6990.000002911029
Missense in Polyphen1824.2560.74209339
Synonymous0.9992431.10.7720.00000148409
Loss of Function0.33244.780.8362.11e-761

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001850.0000181
Middle Eastern0.000.00
South Asian0.0001000.0000989
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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