ZIC5

Zic family member 5, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 13:99962964-99971767

Links

ENSG00000139800 ∙ NCBI:85416 ∙ OMIM:617896 ∙ HGNC:20322 ∙ Uniprot:Q96T25 ∙ 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 ZIC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZIC5 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				4		4
missense			53	6	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel				1	4	5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	54	11	5

Variants in ZIC5

This is a list of pathogenic ClinVar variants found in the ZIC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-99965410-G-A			Likely benign (Mar 01, 2022)
13-99965445-C-T		not specified	Uncertain significance (Apr 07, 2022)
13-99965483-C-G		not specified	Uncertain significance (Nov 12, 2021)
13-99965543-T-A		not specified	Uncertain significance (Jun 01, 2022)
13-99965547-T-C		not specified	Uncertain significance (Feb 26, 2024)
13-99965588-G-A		not specified	Uncertain significance (Nov 18, 2022)
13-99965702-C-T		not specified	Uncertain significance (Sep 14, 2022)
13-99965707-C-T			Likely benign (Nov 17, 2017)
13-99965757-G-A		not specified	Uncertain significance (Jan 06, 2023)
13-99965795-A-C		not specified	Uncertain significance (Apr 06, 2024)
13-99970274-C-G		not specified	Uncertain significance (May 06, 2022)
13-99970359-G-C		not specified	Uncertain significance (Jul 06, 2021)
13-99970411-G-T		not specified	Uncertain significance (Apr 06, 2024)
13-99970412-G-A		not specified	Uncertain significance (Jan 30, 2024)
13-99970413-TGGC-T		not specified	Benign (Dec 31, 2019)
13-99970413-TGGCGGCGGCGGCGGC-T			Likely benign (Dec 07, 2017)
13-99970413-TGGCGGCGGCGGCGGCGGC-T		not specified	Benign (Aug 05, 2015)
13-99970413-TGGCGGCGGCGGCGGCGGCGGC-T			Benign (Oct 13, 2017)
13-99970413-T-TGGC		not specified	Benign (Dec 31, 2019)
13-99970436-G-A		not specified	Uncertain significance (Aug 08, 2023)
13-99970454-C-G		not specified	Uncertain significance (Sep 26, 2023)
13-99970468-G-A		not specified	Uncertain significance (Mar 29, 2024)
13-99970469-G-A		not specified	Uncertain significance (Jun 24, 2022)
13-99970493-C-T		not specified	Uncertain significance (Feb 27, 2024)
13-99970495-T-G		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZIC5	protein_coding	protein_coding	ENST00000267294	2	8946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.765	0.233	125740	0	4	125744	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.963	205	248	0.828	0.0000120	4159
Missense in Polyphen		44	74.57	0.59005		856
Synonymous	0.591	101	109	0.928	0.00000558	1461
Loss of Function	2.50	1	9.14	0.109	4.52e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for neural crest development, converting cells from an epidermal fate to a neural crest cell fate. Binds to DNA (By similarity). {ECO:0000250}.
• Pathway: Neural Crest Differentiation;Mesodermal Commitment Pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.626
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zic5
• 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); vision/eye phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: zic5
• Affected structure: tectal ventricle
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;nervous system development;central nervous system development;cell differentiation
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding