ZC3HC1

zinc finger C3HC-type containing 1, the group of Zinc fingers

Basic information

Region (hg38): 7:130018287-130051401

Links

ENSG00000091732 ∙ NCBI:51530 ∙ OMIM:619746 ∙ HGNC:29913 ∙ Uniprot:Q86WB0 ∙ 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 ZC3HC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3HC1 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						0
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in ZC3HC1

This is a list of pathogenic ClinVar variants found in the ZC3HC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130018692-C-T		not specified	Uncertain significance (Feb 27, 2024)
7-130022321-T-A		not specified	Uncertain significance (May 23, 2024)
7-130022329-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-130022356-T-A		not specified	Uncertain significance (Nov 17, 2023)
7-130022405-C-T		not specified	Likely benign (Feb 16, 2023)
7-130023513-A-C		not specified	Uncertain significance (Mar 07, 2024)
7-130023533-C-T		not specified	Uncertain significance (Feb 14, 2023)
7-130023534-G-A		not specified	Uncertain significance (Dec 06, 2023)
7-130023537-C-G		not specified	Uncertain significance (Feb 06, 2023)
7-130023539-C-T		not specified	Uncertain significance (Jun 30, 2023)
7-130023551-C-T		not specified	Uncertain significance (Jan 10, 2023)
7-130023676-G-C		not specified	Uncertain significance (Sep 07, 2022)
7-130023686-C-T		not specified	Uncertain significance (Jan 26, 2023)
7-130023687-G-A		not specified	Uncertain significance (Aug 04, 2021)
7-130024301-G-A		not specified	Uncertain significance (Nov 28, 2024)
7-130024342-C-T		not specified	Uncertain significance (Jul 10, 2024)
7-130024343-G-A		not specified	Uncertain significance (Oct 20, 2021)
7-130024364-C-G		not specified	Uncertain significance (Mar 06, 2023)
7-130024412-T-C		not specified	Uncertain significance (Dec 19, 2022)
7-130026164-G-A		not specified	Uncertain significance (Sep 10, 2024)
7-130026251-C-A		not specified	Uncertain significance (Feb 15, 2023)
7-130028943-G-A		not specified	Uncertain significance (Nov 28, 2024)
7-130029016-C-T		not specified	Uncertain significance (Dec 09, 2023)
7-130039466-G-T		not specified	Uncertain significance (Feb 15, 2023)
7-130039482-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3HC1	protein_coding	protein_coding	ENST00000358303	10	33166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000256	0.999	125704	0	43	125747	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	234	286	0.818	0.0000154	3264
Missense in Polyphen		58	76.983	0.75341		818
Synonymous	0.257	104	107	0.968	0.00000555	1020
Loss of Function	2.97	11	27.9	0.394	0.00000178	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000291	0.000290
Middle Eastern	0.000220	0.000217
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of a SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry. May have an antiapoptotic role in NPM-ALK-mediated signaling events. {ECO:0000269|PubMed:16009132}.

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.674
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3hc1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial phenotype; reproductive system phenotype; 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); skeleton phenotype

Gene ontology

• Biological process: cell cycle;protein ubiquitination;cell division;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: nucleus;nuclear membrane
• Molecular function: protein binding;zinc ion binding;protein kinase binding