ZCCHC2

protein-coding

zinc finger CCHC-type containing 2, the group of Zinc fingers CCHC-type

Gene summary

Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C18orf49

MANE transcript

NM_017742.6

Inheritance

—

ClinVar variants

U:199B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr18:62,523,025-62,587,709

External References & Databases

Ensembl (ENSG00000141664)

Transcript & Mutation Effects

hg38 • Region Span ~64.7 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 ZCCHC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 199

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017742.6. 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			2 clinvar	3 clinvar		5
missense			193 clinvar	12 clinvar		205
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	199	15	0	214

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017742.6	RefSeq	NP_060212.4	14	MANE Select
ENST00000269499.10	Ensembl	ENSP00000269499.4	14	MANE Select
ENST00000585873.5	Ensembl	ENSP00000468789.1	14	Standard
ENST00000586834.1	Ensembl	ENSP00000464791.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding
zinc ion binding
phosphatidylinositol binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269499
Coding exons: 14
Length: 64703
Individuals with no LoFs: 124612
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 124652
p: 0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.447	516	545	0.946	0.0000271	7511
Missense (PolyPhen)		159	199.61	0.79654		2676
Synonymous	-1.50	250	222	1.13	0.0000124	2462
Loss of Function	5.11	6	41.6	0.144	0.00000219	540

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.0029	0.0028	notable
East Asian	0.00011	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000071	0.000071	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.493
RVIS EVS: 0.34
RVIS percentile EVS: 73.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.881

Gene Damage Prediction

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