ZC3H18

zinc finger CCCH-type containing 18, the group of Zinc fingers CCCH-type

Basic information

Region (hg38): 16:88570402-88631964

Links

ENSG00000158545 ∙ NCBI:124245 ∙ ∙ HGNC:25091 ∙ Uniprot:Q86VM9 ∙ 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 ZC3H18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZC3H18 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	1	4
missense			70	5		75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	8	1

Variants in ZC3H18

This is a list of pathogenic ClinVar variants found in the ZC3H18 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88577166-G-A		not specified	Uncertain significance (Nov 18, 2022)
16-88577193-T-C		not specified	Uncertain significance (Feb 16, 2023)
16-88577199-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-88577212-G-C		not specified	Uncertain significance (Jan 26, 2022)
16-88577225-C-T			Benign (Dec 14, 2017)
16-88577226-G-A		not specified	Uncertain significance (Jun 09, 2022)
16-88577228-T-G		not specified	Likely benign (Jun 01, 2023)
16-88577287-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-88577296-C-T		not specified	Likely benign (Nov 16, 2021)
16-88577319-C-T			Likely benign (May 08, 2018)
16-88577328-G-A		not specified	Uncertain significance (Jan 10, 2022)
16-88577337-C-G		not specified	Uncertain significance (Jul 13, 2021)
16-88577337-C-T		not specified	Uncertain significance (Jun 11, 2024)
16-88577392-G-A		not specified	Uncertain significance (Sep 28, 2022)
16-88577424-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-88577454-G-A		not specified	Uncertain significance (Jun 09, 2022)
16-88577585-T-G		not specified	Uncertain significance (Mar 23, 2023)
16-88577617-A-T		not specified	Uncertain significance (Sep 13, 2023)
16-88577634-G-A		not specified	Uncertain significance (Apr 08, 2024)
16-88577694-G-A		not specified	Uncertain significance (Nov 29, 2023)
16-88598315-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-88598656-C-G		not specified	Uncertain significance (Jan 26, 2023)
16-88598669-C-T		not specified	Uncertain significance (Jun 02, 2023)
16-88599874-A-C		not specified	Uncertain significance (Oct 04, 2022)
16-88599924-T-C		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZC3H18	protein_coding	protein_coding	ENST00000301011	17	61586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.47e-7	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.580	580	621	0.934	0.0000441	6094
Missense in Polyphen		74	99.121	0.74656		1010
Synonymous	-2.96	331	269	1.23	0.0000193	1929
Loss of Function	6.30	2	50.1	0.0399	0.00000295	544

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.216
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.76

Haploinsufficiency Scores

• pHI: 0.432
• hipred: Y
• hipred_score: 0.775
• ghis: 0.652

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.918

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zc3h18

Gene ontology

• Cellular component: nuclear speck;protein-containing complex
• Molecular function: RNA binding;protein binding;metal ion binding