ZC3H8

zinc finger CCCH-type containing 8, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 2:112211529-112255136

Previous symbols: [ "ZC3HDC8" ]

Links

ENSG00000144161 ∙ NCBI:84524 ∙ ∙ HGNC:30941 ∙ Uniprot:Q8N5P1 ∙ 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 ZC3H8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H8 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			8		2	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	2

Variants in ZC3H8

This is a list of pathogenic ClinVar variants found in the ZC3H8 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112230925-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-112231929-A-G		not specified	Uncertain significance (Dec 14, 2022)
2-112233301-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-112233355-A-T		not specified	Uncertain significance (Jun 16, 2024)
2-112234169-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-112234170-G-A		not specified	Uncertain significance (Jul 15, 2021)
2-112234235-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-112236575-C-T			Benign (Feb 26, 2018)
2-112236583-C-A		not specified	Uncertain significance (Feb 22, 2025)
2-112238386-G-A		not specified	Uncertain significance (Jan 15, 2025)
2-112238467-T-C		not specified	Uncertain significance (Aug 10, 2021)
2-112238491-T-C			Benign (Feb 26, 2018)
2-112238497-G-A		not specified	Likely benign (Mar 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H8	protein_coding	protein_coding	ENST00000409573	8	43612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.257	0.742	124625	0	13	124638	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	88	133	0.662	0.00000615	1935
Missense in Polyphen		16	41.616	0.38446		647
Synonymous	0.846	39	46.3	0.842	0.00000232	462
Loss of Function	2.83	4	16.4	0.245	7.70e-7	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000205
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000627	0.0000619
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor of the GATA3 promoter. Sequence-specific DNA-binding factor that binds to the 5'-AGGTCTC-3' sequence within the negative cis-acting element intronic regulatory region (IRR) of the GATA3 gene (By similarity). Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:23932780). Induces thymocyte apoptosis when overexpressed, which may indicate a role in regulation of thymocyte homeostasis. {ECO:0000250, ECO:0000269|PubMed:12077251, ECO:0000269|PubMed:12153508, ECO:0000269|PubMed:23932780}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.480
• hipred: N
• hipred_score: 0.314
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h8

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;apoptotic process;negative regulation of T cell differentiation in thymus;snRNA transcription by RNA polymerase II;snRNA transcription by RNA polymerase III;T cell homeostasis;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase III;response to antibiotic;positive regulation of thymocyte apoptotic process
• Cellular component: nucleus;nucleoplasm;transcription elongation factor complex;Cajal body;nuclear body;transcriptionally active chromatin;histone locus body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;RNA binding;protein binding;sequence-specific DNA binding;metal ion binding