ZIC4

Zic family member 4, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:147386045-147406809

Links

ENSG00000174963 ∙ NCBI:84107 ∙ OMIM:608948 ∙ HGNC:20393 ∙ Uniprot:Q8N9L1 ∙ 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 ZIC4 gene.

• not provided (51 variants)
• Inborn genetic diseases (23 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZIC4 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				13	2	15
missense			33	2	3	38
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			6	7	1	14
Total	0	0	41	22	6

Variants in ZIC4

This is a list of pathogenic ClinVar variants found in the ZIC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-147388874-T-G			Benign (Jan 15, 2024)
3-147390947-C-T			Uncertain significance (Sep 18, 2023)
3-147390964-G-T		not specified	Uncertain significance (Aug 02, 2021)
3-147390967-G-C		not specified	Uncertain significance (Aug 08, 2022)
3-147390969-C-A			Likely benign (Jun 10, 2023)
3-147390969-C-G		not specified	Benign (Jan 29, 2024)
3-147390970-G-A			Benign (Jan 26, 2024)
3-147390970-G-C			Uncertain significance (Mar 31, 2023)
3-147390972-G-A			Likely benign (Jun 11, 2023)
3-147391022-C-G			Uncertain significance (Apr 01, 2023)
3-147391035-C-G			Likely benign (Dec 28, 2023)
3-147391036-G-C			Uncertain significance (Mar 21, 2022)
3-147391060-G-A			Uncertain significance (Sep 09, 2023)
3-147391070-C-A			Uncertain significance (Sep 08, 2023)
3-147391086-C-T			Likely benign (Sep 05, 2023)
3-147391095-C-A			Benign (Jan 22, 2024)
3-147391104-G-A			Likely benign (Oct 25, 2022)
3-147391120-T-C		not specified	Uncertain significance (Apr 07, 2023)
3-147391141-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-147391142-T-G		not specified	Uncertain significance (Aug 04, 2023)
3-147391145-A-G		not specified	Uncertain significance (Sep 13, 2023)
3-147391152-G-C		not specified	Uncertain significance (May 18, 2023)
3-147391159-G-C		not specified	Uncertain significance (Oct 13, 2023)
3-147391170-C-T			Likely benign (May 07, 2023)
3-147391191-G-A			Likely benign (Oct 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZIC4	protein_coding	protein_coding	ENST00000525172	4	20815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000493	0.971	125643	0	63	125706	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.113	230	225	1.02	0.0000108	2481
Missense in Polyphen		95	108.02	0.8795		1162
Synonymous	-1.71	116	94.8	1.22	0.00000464	775
Loss of Function	1.95	8	16.5	0.484	8.97e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00124
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000106
Middle Eastern	0.00	0.00
South Asian	0.000785	0.000784
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to DNA. {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.351
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.438
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zic4
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;central nervous system development
• 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;metal ion binding