HES6

hes family bHLH transcription factor 6, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 2:238238267-238240662

Links

ENSG00000144485 ∙ NCBI:55502 ∙ OMIM:610331 ∙ HGNC:18254 ∙ Uniprot:Q96HZ4 ∙ 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 HES6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HES6 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			19			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	19	0	0

Variants in HES6

This is a list of pathogenic ClinVar variants found in the HES6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-238238864-G-C		not specified	Uncertain significance (Jan 03, 2025)
2-238238889-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-238238901-G-T		not specified	Uncertain significance (Jun 10, 2025)
2-238238912-G-A		not specified	Uncertain significance (Feb 09, 2023)
2-238238913-G-A		not specified	Uncertain significance (Jun 06, 2025)
2-238238978-G-A		not specified	Uncertain significance (Sep 26, 2024)
2-238238991-T-C		not specified	Uncertain significance (Nov 09, 2021)
2-238238993-G-A		not specified	Uncertain significance (Feb 14, 2023)
2-238239019-C-G		not specified	Uncertain significance (Feb 20, 2025)
2-238239035-G-A		not specified	Uncertain significance (Mar 27, 2025)
2-238239050-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-238239053-G-A		not specified	Uncertain significance (May 10, 2022)
2-238239075-C-T		not specified	Uncertain significance (Apr 17, 2025)
2-238239089-C-T		not specified	Uncertain significance (Nov 05, 2021)
2-238239103-C-T		not specified	Uncertain significance (Jan 25, 2024)
2-238239107-G-A		not specified	Uncertain significance (Mar 02, 2023)
2-238239111-C-T		not specified	Uncertain significance (Mar 22, 2025)
2-238239122-T-C		not specified	Uncertain significance (Feb 11, 2025)
2-238239197-T-C		not specified	Uncertain significance (Sep 21, 2023)
2-238239210-C-T		not specified	Uncertain significance (Aug 17, 2021)
2-238239213-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-238239251-T-C		not specified	Uncertain significance (Apr 12, 2025)
2-238239499-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-238239544-C-T		not specified	Uncertain significance (Nov 26, 2024)
2-238239675-G-C		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HES6	protein_coding	protein_coding	ENST00000272937	4	2396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0839	0.771	120659	0	2	120661	0.00000829

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.517	95	110	0.861	0.00000617	1366
Missense in Polyphen		41	45.164	0.90781		515
Synonymous	1.60	37	51.7	0.716	0.00000342	497
Loss of Function	1.07	2	4.44	0.450	1.90e-7	75

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)	0.00000943	0.00000941
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000169	0.000168

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not bind DNA itself but suppresses both HES1- mediated N box-dependent transcriptional repression and binding of HES1 to E box sequences. Also suppresses HES1-mediated inhibition of the heterodimer formed by ASCL1/MASH1 and TCF3/E47, allowing ASCL1 and TCF3 to up-regulate transcription in its presence. Promotes cell differentiation (By similarity). {ECO:0000250}.
• Pathway: Human papillomavirus infection - Homo sapiens (human);Notch Signaling Pathway;Notch;Notch-mediated HES/HEY network (Consensus)

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.600
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hes6

Zebrafish Information Network

• Gene name: hes6
• Affected structure: vertebral column
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;somitogenesis;regulation of transcription, DNA-templated;Notch signaling pathway;cell differentiation;regulation of neurogenesis
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coregulator activity;transcription corepressor activity;transcription factor binding;sequence-specific DNA binding;protein dimerization activity;sequence-specific double-stranded DNA binding