ZC3H4

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

Basic information

Region (hg38): 19:47064187-47113776

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.

• not_specified (183 variants)
• ZC3H4-related_disorder (33 variants)
• not_provided (12 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. These statistics are base on transcript: NM_000015168.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				13	11	24
missense			174	15	1	190
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	174	28	12

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