ZC3H3

zinc finger CCCH-type containing 3, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 8:143437659-143541447

Previous symbols: [ "ZC3HDC3" ]

Links

ENSG00000014164 ∙ NCBI:23144 ∙ OMIM:618640 ∙ HGNC:28972 ∙ Uniprot:Q8IXZ2 ∙ 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 ZC3H3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H3 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				3		3
missense			105	12	1	118
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	105	15	1

Variants in ZC3H3

This is a list of pathogenic ClinVar variants found in the ZC3H3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143440045-G-A			Likely benign (Jul 01, 2022)
8-143440052-G-C		not specified	Uncertain significance (Mar 30, 2024)
8-143440073-C-T		not specified	Uncertain significance (Feb 20, 2025)
8-143440077-C-A			Benign (Aug 30, 2018)
8-143440108-C-G			Likely benign (Oct 01, 2022)
8-143440166-G-T		not specified	Uncertain significance (Apr 08, 2022)
8-143440229-G-A		not specified	Uncertain significance (Nov 27, 2023)
8-143440253-G-A		not specified	Likely benign (Sep 11, 2024)
8-143440262-G-A		not specified	Uncertain significance (Apr 16, 2024)
8-143440304-G-A		not specified	Uncertain significance (May 20, 2024)
8-143440304-G-C		not specified	Uncertain significance (Mar 29, 2022)
8-143440319-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-143440359-G-A		not specified	Likely benign (Apr 21, 2022)
8-143440954-G-A		not specified	Uncertain significance (Oct 07, 2024)
8-143440979-C-T		not specified	Uncertain significance (Sep 08, 2024)
8-143440999-G-A		not specified	Uncertain significance (Jul 17, 2024)
8-143441002-G-A		not specified	Uncertain significance (Mar 07, 2023)
8-143441023-C-T			Likely benign (Jan 01, 2023)
8-143441024-G-A		not specified	Uncertain significance (Dec 01, 2022)
8-143441026-T-A		not specified	Uncertain significance (Sep 07, 2022)
8-143441035-C-T		not specified	Uncertain significance (Dec 13, 2022)
8-143441041-A-G		not specified	Uncertain significance (Jan 23, 2025)
8-143441062-C-T		not specified	Uncertain significance (Jan 22, 2024)
8-143441071-G-A		not specified	Likely benign (Nov 14, 2023)
8-143441072-C-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H3	protein_coding	protein_coding	ENST00000262577	12	103799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.470	0.530	125685	0	27	125712	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00625	592	592	1.00	0.0000400	5928
Missense in Polyphen		162	186.27	0.8697		1755
Synonymous	-2.88	314	255	1.23	0.0000171	2113
Loss of Function	4.10	7	32.1	0.218	0.00000152	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000491	0.0000462
European (Non-Finnish)	0.0000911	0.0000879
Middle Eastern	0.000164	0.000163
South Asian	0.000104	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the export of polyadenylated mRNAs from the nucleus (PubMed:19364924). Enhances ACVR1B-induced SMAD-dependent transcription. Binds to single-stranded DNA but not to double- stranded DNA in vitro. Involved in RNA cleavage (By similarity). {ECO:0000250|UniProtKB:Q8CHP0, ECO:0000269|PubMed:19364924}.

Recessive Scores

• pRec: 0.0960

Intolerance Scores

• loftool: 0.485
• rvis_EVS: 2.68
• rvis_percentile_EVS: 98.86

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.273
• ghis: 0.408

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h3

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;mRNA polyadenylation;regulation of mRNA export from nucleus;poly(A)+ mRNA export from nucleus;positive regulation of activin receptor signaling pathway
• Cellular component: nucleus;mRNA cleavage and polyadenylation specificity factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;metal ion binding;R-SMAD binding