HIC2

HIC ZBTB transcriptional repressor 2, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 22:21417371-21451463

Links

ENSG00000169635 ∙ NCBI:23119 ∙ OMIM:607712 ∙ HGNC:18595 ∙ Uniprot:Q96JB3 ∙ 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 HIC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIC2 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				1	1	2
missense			55	1		56
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	2	1

Variants in HIC2

This is a list of pathogenic ClinVar variants found in the HIC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21442850-G-T		not specified	Uncertain significance (Jun 17, 2024)
22-21444923-T-C		not specified	Uncertain significance (Feb 27, 2024)
22-21444925-G-C		not specified	Uncertain significance (Jan 29, 2025)
22-21444929-G-A		not specified	Uncertain significance (Jul 30, 2023)
22-21444930-C-T		not specified	Uncertain significance (Jun 30, 2022)
22-21444944-G-A		not specified	Uncertain significance (Aug 11, 2024)
22-21444953-G-A		not specified	Uncertain significance (Nov 26, 2024)
22-21444971-C-T		not specified	Uncertain significance (Feb 10, 2023)
22-21445040-A-G		not specified	Uncertain significance (Feb 22, 2025)
22-21445054-G-C		not specified	Uncertain significance (Dec 28, 2023)
22-21445261-C-T			Likely benign (Feb 01, 2023)
22-21445308-A-G		not specified	Uncertain significance (May 25, 2022)
22-21445347-C-T		not specified	Likely benign (Mar 22, 2023)
22-21445368-G-A		not specified	Uncertain significance (Jul 20, 2022)
22-21445385-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-21445415-C-T			Likely benign (Mar 01, 2025)
22-21445416-G-A		not specified	Uncertain significance (Feb 26, 2025)
22-21445425-G-C		not specified	Uncertain significance (Jan 23, 2024)
22-21445440-G-T		not specified	Uncertain significance (May 30, 2024)
22-21445455-C-T		not specified	Uncertain significance (Oct 30, 2023)
22-21445466-C-T		not specified	Uncertain significance (Dec 02, 2022)
22-21445488-A-G		not specified	Uncertain significance (Nov 07, 2022)
22-21445489-C-G		not specified	Uncertain significance (Aug 21, 2024)
22-21445541-C-T		not specified	Uncertain significance (Nov 17, 2023)
22-21445550-T-A		not specified	Uncertain significance (Feb 14, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIC2	protein_coding	protein_coding	ENST00000443632	2	34060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00332	123229	0	2	123231	0.00000811

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	282	397	0.710	0.0000268	3974
Missense in Polyphen		32	80.536	0.39734		643
Synonymous	-2.34	217	177	1.22	0.0000133	1265
Loss of Function	3.80	0	16.8	0.00	7.98e-7	193

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)	0.00000903	0.00000903
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000329
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.0150
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.660
• hipred: Y
• hipred_score: 0.768
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hic2
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;protein C-terminus binding;metal ion binding