ZC3H7A

protein-coding

zinc finger CCCH-type containing 7A, the group of Zinc fingers CCCH-type|Tetratricopeptide repeat domain containing

Gene summary

Enables miRNA binding activity. Involved in miRNA processing. Acts upstream of with a positive effect on post-transcriptional regulation of gene expression. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZC3HDC7
ZC3H7

MANE transcript

NM_014153.4

Inheritance

—

ClinVar variants

U:123B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr16:11,750,586-11,797,258

External References & Databases

Ensembl (ENSG00000122299)

Transcript & Mutation Effects

hg38 • Region Span ~46.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZC3H7A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 113

not providedTotal: 3

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014153.4. 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			4
missense			112 clinvar	6 clinvar		118
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	123	6	0	129

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014153.4	RefSeq	NP_054872.2	22	MANE Select
ENST00000355758.9	Ensembl	ENSP00000347999.4	22	MANE Select
ENST00000396516.6	Ensembl	ENSP00000379773.2	22	Standard
ENST00000396516.7	Ensembl	ENSP00000379773.2	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

posttranscriptional regulation of gene expression
production of miRNAs involved in gene silencing by miRNA

Molecular Function

RNA binding
miRNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396516
Coding exons: 22
Length: 46682
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125742
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.75	406	518	0.784	0.0000274	6428
Missense (PolyPhen)		89	202.12	0.44032		2432
Synonymous	-0.638	193	182	1.06	0.0000103	1707
Loss of Function	6.62	2	54.9	0.0364	0.00000277	715

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000091	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000044	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a specific regulator of miRNA biogenesis. Binds to microRNAs MIR7-1, MIR16-2 and MIR29A hairpins recognizing the 3'-ATA(A/T)-5' motif in the apical loop. {ECO:0000269|PubMed:28431233}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.0927
RVIS EVS: -0.39
RVIS percentile EVS: 27.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.934

Gene Damage Prediction

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