ZC3H15

protein-coding

zinc finger CCCH-type containing 15, the group of Zinc fingers CCCH-type

Gene summary

Enables RNA binding activity and cadherin binding activity. Involved in positive regulation of GTPase activity. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018471.3

Inheritance

—

ClinVar variants

U:36B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr2:186,486,253-186,511,929

External References & Databases

Ensembl (ENSG00000065548)

Transcript & Mutation Effects

hg38 • Region Span ~25.7 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 ZC3H15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 32

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018471.3. 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			1 clinvar			1
missense			32 clinvar	1 clinvar		33
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	36	1	0	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018471.3	RefSeq	NP_060941.2	10	MANE Select
ENST00000337859.11	Ensembl	ENSP00000338788.6	10	MANE Select
ENST00000421536.5	Ensembl	ENSP00000410981.1	4	Standard
ENST00000437396.1	Ensembl	ENSP00000407192.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cytoplasmic translation
regulation of transcription by RNA polymerase II
cytokine-mediated signaling pathway

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA binding
protein binding
cadherin binding
metal ion binding

Cellular Component

nucleolus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337859
Coding exons: 10
Length: 23208
Individuals with no LoFs: 124781
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124792
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.83	136	211	0.645	0.0000103	2848
Missense (PolyPhen)		16	49.556	0.32287		743
Synonymous	0.264	68	70.8	0.960	0.00000347	715
Loss of Function	3.61	3	20.7	0.145	9.54e-7	301

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Protects DRG1 from proteolytic degradation. {ECO:0000250}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.315
RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.279

Gene Damage Prediction

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