HES3

hes family bHLH transcription factor 3, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:6244179-6245578

Links

ENSG00000173673 ∙ NCBI:390992 ∙ OMIM:609971 ∙ HGNC:26226 ∙ Uniprot:Q5TGS1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HES3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HES3 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	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in HES3

This is a list of pathogenic ClinVar variants found in the HES3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-6244396-G-C		not specified	Uncertain significance (Nov 10, 2024)
1-6244552-G-A		not specified	Likely benign (May 23, 2024)
1-6244558-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-6245127-A-G		not specified	Uncertain significance (Mar 01, 2023)
1-6245136-G-C		not specified	Uncertain significance (Jan 18, 2025)
1-6245143-C-A		not specified	Uncertain significance (Oct 17, 2024)
1-6245143-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-6245184-C-A		not specified	Uncertain significance (Sep 29, 2023)
1-6245191-G-A		not specified	Uncertain significance (Mar 08, 2024)
1-6245217-C-T		not specified	Uncertain significance (Feb 14, 2024)
1-6245247-G-C		not specified	Uncertain significance (Feb 14, 2024)
1-6245254-C-A		not specified	Uncertain significance (Aug 19, 2023)
1-6245268-G-T		not specified	Uncertain significance (May 04, 2025)
1-6245284-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-6245290-C-T		not specified	Uncertain significance (Apr 17, 2025)
1-6245317-T-G		not specified	Uncertain significance (Sep 15, 2021)
1-6245361-C-T		not specified	Uncertain significance (May 31, 2022)
1-6245383-G-A		not specified	Uncertain significance (Apr 14, 2025)
1-6245395-C-T		not specified	Uncertain significance (Jun 05, 2024)
1-6245440-C-T		not specified	Uncertain significance (Jun 07, 2025)
1-6245458-G-A		not specified	Uncertain significance (Nov 07, 2024)
1-6245473-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-6245495-T-A		not specified	Uncertain significance (Apr 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HES3	protein_coding	protein_coding	ENST00000377898	3	1387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.277	0.641	124744	0	5	124749	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.577	68	82.8	0.821	0.00000386	1128
Missense in Polyphen		23	28.293	0.81292		338
Synonymous	-1.05	46	37.8	1.22	0.00000182	395
Loss of Function	1.31	1	3.72	0.269	1.55e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

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)

Haploinsufficiency Scores

• pHI: 0.402
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hes3
• Phenotype: cellular phenotype; growth/size/body region 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); 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; embryo phenotype

Zebrafish Information Network

• Gene name: her3
• Affected structure: rhombomere 4
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;somitogenesis;Notch signaling pathway;midbrain-hindbrain boundary morphogenesis;oculomotor nerve development;trochlear nerve development;hindbrain morphogenesis;cell differentiation;midbrain development;positive regulation of transcription by RNA polymerase II;regulation of neurogenesis;regulation of timing of neuron differentiation
• 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