CIZ1

CDKN1A interacting zinc finger protein 1

Basic information

Region (hg38): 9:128161250-128204383

Links

ENSG00000148337 ∙ NCBI:25792 ∙ OMIM:611420 ∙ HGNC:16744 ∙ Uniprot:Q9ULV3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dystonia 23 (Moderate), mode of inheritance: Unknown
• inherited dystonia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Primary cervical dystonia, adult-onset	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	22447717

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CIZ1 gene.

• Dystonic disorder (242 variants)
• not provided (40 variants)
• Inborn genetic diseases (35 variants)
• Dystonia 23 (1 variants)
• Dystonia, primary cervical (1 variants)
• Variant of unknown significance (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIZ1 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	48	18	70
missense			115	9	10	134
nonsense			1			1
start loss						0
frameshift						0
inframe indel			15			15
splice donor/acceptor (+/-2bp)			1			1
splice region			5	4	1	10
non coding				18	33	51
Total	0	0	136	75	61

Variants in CIZ1

This is a list of pathogenic ClinVar variants found in the CIZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128166207-A-G		Dystonic disorder	Uncertain significance (Jan 11, 2023)
9-128166213-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-128166220-G-A		Dystonic disorder	Uncertain significance (Jul 05, 2023)
9-128166242-G-A		Dystonic disorder	Likely benign (Nov 27, 2023)
9-128166246-C-T		Dystonic disorder	Uncertain significance (Jun 29, 2023)
9-128166251-C-T		Dystonic disorder	Likely benign (Nov 17, 2023)
9-128166252-G-A		Dystonic disorder	Uncertain significance (Nov 27, 2023)
9-128166258-T-C		Dystonic disorder	Uncertain significance (Oct 18, 2022)
9-128166268-T-C		Dystonic disorder	Uncertain significance (Dec 11, 2023)
9-128166278-G-T		Dystonic disorder	Likely benign (Apr 29, 2022)
9-128166299-G-C			Likely benign (Jan 01, 2023)
9-128166300-C-T		Dystonic disorder • not specified	Uncertain significance (May 05, 2023)
9-128166305-G-A		Dystonic disorder	Likely benign (May 20, 2023)
9-128166321-G-A		Dystonic disorder	Uncertain significance (Apr 17, 2019)
9-128166331-C-A		Dystonic disorder	Uncertain significance (Jan 26, 2024)
9-128166331-C-T		not specified	Uncertain significance (Dec 17, 2023)
9-128166332-G-A		Dystonic disorder • CIZ1-related disorder	Benign/Likely benign (Jan 29, 2024)
9-128166341-G-A		Dystonic disorder	Likely benign (May 05, 2023)
9-128166354-C-T		Dystonic disorder	Benign (Jan 25, 2024)
9-128166374-G-A		Dystonic disorder	Likely benign (Mar 12, 2023)
9-128166389-C-A		not specified	Uncertain significance (Jun 21, 2023)
9-128166396-G-C		Dystonic disorder • not specified	Uncertain significance (Oct 26, 2022)
9-128166401-G-A		Dystonic disorder	Likely benign (Mar 14, 2023)
9-128166404-T-C		Dystonic disorder	Likely benign (Oct 16, 2018)
9-128166416-G-A		Dystonic disorder	Likely benign (Jan 24, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIZ1	protein_coding	protein_coding	ENST00000393608	16	38320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0632	0.937	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	371	496	0.749	0.0000286	5780
Missense in Polyphen		69	122.98	0.56105		1423
Synonymous	0.788	187	201	0.929	0.0000120	1773
Loss of Function	4.98	13	51.7	0.252	0.00000255	526

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000816	0.000816
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000797	0.0000791
Middle Eastern	0.000816	0.000816
South Asian	0.000100	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the subcellular localization of CIP/WAF1.
• Disease: DISEASE: Note=Defects in CIZ1 may be a cause of adult onset primary cervical dystonia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. Cervical dystonia or spasmodic torticollis, the most common form of focal dystonia, is characterized by involuntary contractions of the neck muscles, which produce abnormal posturing of the head upon the trunk.

Recessive Scores

• pRec: 0.0907

Intolerance Scores

• loftool: 0.576
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.281
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ciz1
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; growth/size/body region phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Cellular component: nucleus;nucleoplasm;plasma membrane
• Molecular function: nucleic acid binding;protein binding;zinc ion binding