ZC3H6

zinc finger CCCH-type containing 6, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 2:112275597-112340059

Previous symbols: [ "ZC3HDC6" ]

Links

ENSG00000188177 ∙ NCBI:376940 ∙ ∙ HGNC:24762 ∙ Uniprot:P61129 ∙ 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 ZC3H6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H6 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			65	2		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	65	5	0

Variants in ZC3H6

This is a list of pathogenic ClinVar variants found in the ZC3H6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-112276011-A-C		not specified	Uncertain significance (Jan 22, 2024)
2-112299859-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-112299893-T-C		not specified	Uncertain significance (Jun 08, 2022)
2-112299977-A-C		not specified	Uncertain significance (Dec 06, 2021)
2-112299980-A-G		not specified	Uncertain significance (Aug 27, 2024)
2-112299995-A-G		not specified	Uncertain significance (Dec 11, 2024)
2-112300014-A-C		not specified	Uncertain significance (Dec 23, 2024)
2-112300015-C-T		not specified	Uncertain significance (Jan 27, 2025)
2-112303230-A-G		not specified	Uncertain significance (Jun 22, 2021)
2-112303257-C-T		not specified	Uncertain significance (May 26, 2024)
2-112303317-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-112303329-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-112303344-T-G		not specified	Uncertain significance (May 29, 2024)
2-112309886-G-A		not specified	Likely benign (Dec 19, 2022)
2-112309993-G-A		not specified	Uncertain significance (Jul 29, 2022)
2-112310017-G-T		not specified	Uncertain significance (Dec 15, 2023)
2-112310027-G-T		not specified	Uncertain significance (Oct 16, 2023)
2-112310057-A-C		not specified	Uncertain significance (Aug 05, 2024)
2-112310058-G-C		not specified	Uncertain significance (Aug 05, 2024)
2-112310073-G-A			Likely benign (Mar 01, 2022)
2-112310087-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-112311822-A-G		not specified	Uncertain significance (May 28, 2024)
2-112311845-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-112311848-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-112311849-G-A		not specified	Uncertain significance (Apr 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H6	protein_coding	protein_coding	ENST00000409871	12	64470

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.192	0.808	124604	0	34	124638	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	482	582	0.828	0.0000274	7808
Missense in Polyphen		116	181.75	0.63824		2613
Synonymous	-0.467	220	211	1.04	0.0000109	2252
Loss of Function	4.56	10	41.8	0.239	0.00000186	637

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000326
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.0000562	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000159
Middle Eastern	0.0000562	0.0000556
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0948

Intolerance Scores

• loftool: 0.519
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.479
• hipred: N
• hipred_score: 0.423
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h6

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process;negative regulation of transcription, DNA-templated
• Cellular component: cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding;molecular_function;DNA-binding transcription factor activity;metal ion binding