CASZ1

castor zinc finger 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:10636603-10796650

Links

ENSG00000130940 ∙ NCBI:54897 ∙ OMIM:609895 ∙ HGNC:26002 ∙ Uniprot:Q86V15 ∙ 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 CASZ1 gene.

• not provided (247 variants)
• Inborn genetic diseases (66 variants)
• CASZ1-related condition (4 variants)
• Primary dilated cardiomyopathy (2 variants)
• not specified (1 variants)
• Neutrophil inclusion bodies (1 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASZ1 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			2	73	28	103
missense			116	12	16	144
nonsense						0
start loss						0
frameshift	1		1			2
inframe indel			11	3	1	15
splice donor/acceptor (+/-2bp)						0
splice region				4	5	9
non coding				10	30	40
Total	1	0	130	98	75

Variants in CASZ1

This is a list of pathogenic ClinVar variants found in the CASZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-10638911-A-AGGCCGC			Benign (May 11, 2021)
1-10638946-G-A			Uncertain significance (Oct 31, 2021)
1-10638951-G-A			Likely benign (Mar 14, 2021)
1-10638954-G-C			Likely benign (Feb 14, 2022)
1-10638962-T-A		not specified	Uncertain significance (Apr 22, 2022)
1-10638979-G-T			Uncertain significance (Jul 31, 2023)
1-10638985-A-G		not specified	Uncertain significance (May 11, 2022)
1-10638988-G-C			Uncertain significance (Sep 06, 2023)
1-10638997-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-10639009-G-C			Benign (Jan 31, 2024)
1-10639015-C-T		not specified	Uncertain significance (Oct 31, 2021)
1-10639017-C-T			Likely benign (Oct 04, 2023)
1-10639053-C-A			Likely benign (Aug 13, 2022)
1-10639058-A-G		not specified	Uncertain significance (Aug 02, 2022)
1-10639060-T-G		not specified	Uncertain significance (Aug 02, 2022)
1-10639067-A-G		not specified	Uncertain significance (Mar 01, 2023)
1-10639068-G-T			Benign (Jun 06, 2023)
1-10639079-GGTCCTCGTCGTCGTC-G			Uncertain significance (Nov 10, 2021)
1-10639079-GGTCCTCGTCGTCGTCGTCCTCGTCGTC-G			Uncertain significance (Jun 15, 2022)
1-10639083-CTCGTCG-C		Neutrophil inclusion bodies	Benign (Jan 31, 2024)
1-10639083-C-CTCG			Uncertain significance (Jul 02, 2022)
1-10639086-GTCGTCGTCGTCC-G		CASZ1-related disorder	Likely benign (Jan 28, 2024)
1-10639086-G-GTCGTCGTCGTCC			Uncertain significance (Sep 08, 2023)
1-10639098-CTCGTCGTCGTCCTCG-C			Uncertain significance (Dec 13, 2023)
1-10639100-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASZ1	protein_coding	protein_coding	ENST00000377022	18	160047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.10e-7	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	866	1.11e+3	0.780	0.0000782	11414
Missense in Polyphen		387	576.91	0.67082		5772
Synonymous	0.499	508	523	0.972	0.0000438	3571
Loss of Function	6.72	4	60.3	0.0663	0.00000293	718

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator (PubMed:23639441, PubMed:27693370). Involved in vascular assembly and morphogenesis through direct transcriptional regulation of EGFL7 (PubMed:23639441). {ECO:0000269|PubMed:23639441, ECO:0000269|PubMed:27693370}.

Recessive Scores

• pRec: 0.275

Intolerance Scores

• loftool: 0.00200
• rvis_EVS: -2.42
• rvis_percentile_EVS: 1.06

Haploinsufficiency Scores

• pHI: 0.717
• hipred: Y
• hipred_score: 0.752
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.532

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Casz1
• Phenotype: liver/biliary system 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); immune system phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;positive regulation of transcription, DNA-templated
• Cellular component: nucleoplasm;cytosol;intracellular membrane-bounded organelle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding