CIZ1

CDKN1A interacting zinc finger protein 1

Basic information

Region (hg38): 9:128161251-128204383

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 (306 variants)
not_specified (95 variants)
not_provided (37 variants)
CIZ1-related_disorder (10 variants)
Dystonia,_primary_cervical (1 variants)
Variant_of_unknown_significance (1 variants)
Dystonia_23 (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. These statistics are base on transcript: NM_001131016.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	75 clinvar	15 clinvar	93
missense			171 clinvar	21 clinvar	7 clinvar	199
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	176	96	22

Loading clinvar variants...

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

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