ZCCHC4

zinc finger CCHC-type containing 4, the group of Zinc fingers CCHC-type|Zinc fingers GRF-type|7BS N6-adenosine DNA/RNA methyltransferases

Basic information

Region (hg38): 4:25312773-25370383

Links

ENSG00000168228 ∙ NCBI:29063 ∙ OMIM:611792 ∙ HGNC:22917 ∙ Uniprot:Q9H5U6 ∙ 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 ZCCHC4 gene.

• Inborn genetic diseases (19 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZCCHC4 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				1		1
missense			19		4	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	1	4

Variants in ZCCHC4

This is a list of pathogenic ClinVar variants found in the ZCCHC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-25312819-T-A		not specified	Uncertain significance (Aug 23, 2021)
4-25312898-C-T			Benign (Dec 31, 2019)
4-25312907-C-G		not specified	Uncertain significance (Jun 24, 2022)
4-25312912-G-A		not specified	Uncertain significance (Dec 28, 2022)
4-25314064-T-C		not specified	Uncertain significance (Dec 02, 2021)
4-25314112-C-T		not specified	Uncertain significance (Nov 08, 2022)
4-25314130-A-G		not specified	Uncertain significance (Jun 09, 2022)
4-25314159-G-C		not specified	Uncertain significance (Feb 10, 2022)
4-25315363-T-C		not specified	Uncertain significance (Dec 04, 2023)
4-25333229-C-G		not specified	Uncertain significance (Nov 29, 2023)
4-25333296-A-G			Benign (Dec 31, 2019)
4-25333328-C-A			Benign (Dec 31, 2019)
4-25333946-A-C		not specified	Uncertain significance (Jan 26, 2022)
4-25345572-T-C			Likely benign (Oct 01, 2022)
4-25349585-C-G		not specified	Uncertain significance (Jul 20, 2021)
4-25351693-G-A			Benign (Dec 31, 2019)
4-25361876-T-A		not specified	Uncertain significance (Jan 27, 2022)
4-25361892-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-25361917-C-T		not specified	Uncertain significance (Oct 26, 2021)
4-25361919-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-25361974-G-C		not specified	Uncertain significance (Oct 26, 2021)
4-25362227-T-G		not specified	Uncertain significance (Jul 15, 2021)
4-25362237-C-G		not specified	Uncertain significance (Jun 03, 2022)
4-25362237-C-T			Benign (Dec 31, 2019)
4-25362245-C-T		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZCCHC4	protein_coding	protein_coding	ENST00000302874	13	57599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-10	0.866	124443	0	355	124798	0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0104	274	274	0.998	0.0000138	3393
Missense in Polyphen		48	56.265	0.85311		670
Synonymous	0.934	87	98.8	0.880	0.00000515	907
Loss of Function	1.78	20	30.6	0.653	0.00000170	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00222
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.00107	0.00106
Finnish	0.000232	0.000232
European (Non-Finnish)	0.00195	0.00193
Middle Eastern	0.00107	0.00106
South Asian	0.000681	0.000621
Other	0.00182	0.00182

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a methyltransferase.

Recessive Scores

• pRec: 0.0910

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.92

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.371
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zcchc4

Gene ontology

• Biological process: methylation
• Molecular function: nucleic acid binding;methyltransferase activity;zinc ion binding;transferase activity, transferring acyl groups