ZC3H4

zinc finger CCCH-type containing 4, the group of Zinc fingers CCCH-type|Armadillo like helical domain containing

Basic information

Region (hg38): 19:47064186-47113776

Previous symbols: [ "C19orf7" ]

Links

ENSG00000130749 ∙ NCBI:23211 ∙ OMIM:619498 ∙ HGNC:17808 ∙ Uniprot:Q9UPT8 ∙ 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 ZC3H4 gene.

• Inborn genetic diseases (58 variants)
• not provided (12 variants)
• ZC3H4-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H4 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				4	6	10
missense			57	2		59
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	57	6	8

Variants in ZC3H4

This is a list of pathogenic ClinVar variants found in the ZC3H4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47066363-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-47066369-G-C		ZC3H4-related disorder	Uncertain significance (Aug 25, 2022)
19-47066434-G-A		ZC3H4-related disorder	Benign (Feb 07, 2020)
19-47066499-C-T		not specified	Uncertain significance (Nov 06, 2023)
19-47066522-T-C		not specified	Uncertain significance (Aug 02, 2022)
19-47066568-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-47066569-G-A		ZC3H4-related disorder	Benign (Feb 04, 2020)
19-47066580-C-T		not specified	Likely benign (May 31, 2023)
19-47066583-G-A		not specified	Uncertain significance (Jan 19, 2024)
19-47066585-G-C		ZC3H4-related disorder	Benign (Nov 25, 2019)
19-47066610-G-A		not specified	Uncertain significance (Apr 25, 2023)
19-47066643-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-47066656-G-A		ZC3H4-related disorder	Benign (Dec 24, 2019)
19-47066697-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-47066766-C-T		not specified	Uncertain significance (Dec 15, 2022)
19-47066768-G-A		ZC3H4-related disorder	Likely benign (Apr 11, 2022)
19-47066800-C-T		ZC3H4-related disorder	Likely benign (Jan 06, 2020)
19-47066875-C-G			Benign (Jan 19, 2018)
19-47066942-G-A		ZC3H4-related disorder	Benign (Oct 30, 2019)
19-47066949-C-T		ZC3H4-related disorder	Likely benign (Jun 12, 2022)
19-47066961-G-A		ZC3H4-related disorder	Likely benign (Apr 11, 2023)
19-47066963-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-47066983-G-A			Likely benign (Nov 09, 2018)
19-47066990-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-47067072-C-T		not specified	Uncertain significance (Jun 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H4	protein_coding	protein_coding	ENST00000253048	14	49566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.38e-9	124783	0	7	124790	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	746	798	0.935	0.0000542	8378
Missense in Polyphen		95	115.73	0.8209		1145
Synonymous	-4.37	446	343	1.30	0.0000253	2661
Loss of Function	6.85	0	54.6	0.00	0.00000377	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.0000994
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000639	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000661	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0635
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.78

Haploinsufficiency Scores

• pHI: 0.400
• hipred: Y
• hipred_score: 0.580
• ghis: 0.581

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.582

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h4
• Phenotype: growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;cytosol
• 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 factor activity;RNA binding;metal ion binding