ZC3H18

protein-coding

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

Gene summary

Enables mRNA cap binding complex binding activity and protein-macromolecule adaptor activity. Involved in RNA destabilization. Located in nuclear speck. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144604.4

Inheritance

—

ClinVar variants

U:160B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr16:88,570,403-88,631,964

External References & Databases

Ensembl (ENSG00000158545)

Transcript & Mutation Effects

hg38 • Region Span ~61.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZC3H18 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 152

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144604.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar	1 clinvar	8
missense			150 clinvar	7 clinvar		157
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	160	10	1	171

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144604.4	RefSeq	NP_653205.3	17	MANE Select
ENST00000301011.10	Ensembl	ENSP00000301011.5	17	MANE Select
NM_001294340.2	RefSeq	NP_001281269.1	18	Standard
ENST00000452588.6	Ensembl	ENSP00000416951.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
protein binding
metal ion binding

Cellular Component

nuclear speck
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301011
Coding exons: 17
Length: 61586
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.580	580	621	0.934	0.0000441	6094
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.216
RVIS EVS: -1.32
RVIS percentile EVS: 4.76

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.918

Gene Damage Prediction

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