HES4

hes family bHLH transcription factor 4, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:998961-1000172

Links

ENSG00000188290 ∙ NCBI:57801 ∙ OMIM:608060 ∙ HGNC:24149 ∙ Uniprot:Q9HCC6 ∙ 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 HES4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HES4 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	28	0	0

Variants in HES4

This is a list of pathogenic ClinVar variants found in the HES4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-999087-C-G		not specified	Uncertain significance (Nov 12, 2021)
1-999090-G-C		not specified	Uncertain significance (Aug 30, 2021)
1-999096-T-A		not specified	Uncertain significance (Oct 13, 2021)
1-999105-G-C		not specified	Uncertain significance (Jul 27, 2021)
1-999111-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-999120-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-999121-G-A		not specified	Uncertain significance (May 14, 2024)
1-999126-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-999127-C-G		not specified	Uncertain significance (Apr 23, 2024)
1-999129-C-A		not specified	Uncertain significance (May 27, 2022)
1-999153-G-C		not specified	Uncertain significance (Jul 27, 2022)
1-999166-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-999244-G-C		not specified	Uncertain significance (Apr 28, 2022)
1-999274-C-G		not specified	Uncertain significance (Feb 27, 2023)
1-999289-A-C		not specified	Uncertain significance (Jun 07, 2024)
1-999295-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-999364-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-999365-C-G		not specified	Uncertain significance (Jul 13, 2022)
1-999538-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-999571-T-C		not specified	Uncertain significance (Jun 07, 2023)
1-999595-G-C		not specified	Uncertain significance (Aug 22, 2023)
1-999602-G-C		not specified	Uncertain significance (Feb 13, 2024)
1-999700-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-999720-G-A		not specified	Uncertain significance (May 05, 2023)
1-999772-T-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HES4	protein_coding	protein_coding	ENST00000428771	3	1211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000137	0.130	124573	0	44	124617	0.000177

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.470	103	90.4	1.14	0.00000414	1473
Missense in Polyphen		30	30.382	0.98741		389
Synonymous	-1.37	53	41.8	1.27	0.00000199	588
Loss of Function	-1.22	6	3.53	1.70	1.53e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000226	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00110	0.00105
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000116
Middle Eastern	0.00110	0.00105
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Binds DNA on N-box motifs: 5'-CACNAG-3' (By similarity). {ECO:0000250}.
• Pathway: Human papillomavirus infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.119

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.285
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

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;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