ZCWPW2

protein-coding

zinc finger CW-type and PWWP domain containing 2, the group of Zinc fingers CW-type|PWWP domain containing

Gene summary

Enables histone H3K4me3 reader activity. Predicted to be involved in chromatin organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001040432.4

Inheritance

—

ClinVar variants

U:70B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr3:28,348,721-28,538,122

External References & Databases

Ensembl (ENSG00000206559)

Transcript & Mutation Effects

hg38 • Region Span ~189.4 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 ZCWPW2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 66

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040432.4. 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			1 clinvar			1
missense			67 clinvar	3 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	70	3	0	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040432.4	RefSeq	NP_001035522.1	8	MANE Select
ENST00000383768.7	Ensembl	ENSP00000373278.2	8	MANE Select
NM_001324169.2	RefSeq	NP_001311098.1	8	Standard
NM_001324170.2	RefSeq	NP_001311099.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

zinc ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383768
Coding exons: 8
Length: 188977
Individuals with no LoFs: 125676
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 125738
p: 0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.906	204	171	1.20	0.00000774	2341
Missense (PolyPhen)		33	40.759	0.80963		546
Synonymous	-0.822	70	61.8	1.13	0.00000307	585
Loss of Function	1.47	12	18.9	0.636	7.87e-7	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00049	0.00049	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00010	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.860
RVIS EVS: 0.37
RVIS percentile EVS: 75.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0402

Gene Damage Prediction

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