HES2

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

Basic information

Region (hg38): 1:6412418-6424670

Links

ENSG00000069812 ∙ NCBI:54626 ∙ OMIM:609970 ∙ HGNC:16005 ∙ Uniprot:Q9Y543 ∙ 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 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			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	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: gnomAD

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: 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

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

Mouse Genome Informatics

• Gene name: Hes2

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