ZCWPW1

protein-coding

zinc finger CW-type and PWWP domain containing 1, the group of Zinc fingers CW-type|PWWP domain containing

Gene summary

Enables histone H3K4me3 reader activity. Involved in epigenetic regulation of gene expression. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001386010.1

Inheritance

—

ClinVar variants

U:91B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr7:100,400,826-100,428,992

External References & Databases

Ensembl (ENSG00000078487)

Transcript & Mutation Effects

hg38 • Region Span ~28.2 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 ZCWPW1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001386010.1. 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 clinvar		2
missense			86 clinvar	7 clinvar	1 clinvar	94
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	91	8	1	100

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 84 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001386010.1	RefSeq	NP_001372939.1	16	MANE Select
ENST00000684423.1	Ensembl	ENSP00000507762.1	16	MANE Select
NM_001258008.3	RefSeq	NP_001244937.1	14	Standard
NM_001386008.1	RefSeq	NP_001372937.1	7	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: ENST00000398027
Coding exons: 16
Length: 28167
Individuals with no LoFs: 124739
Homozygous LoFs: 1
Heterozygous LoFs: 54
Defined: 124794
p: 0.000220

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.13	286	345	0.829	0.0000175	4251
Missense (PolyPhen)		58	84.253	0.68841		1100
Synonymous	0.766	116	127	0.913	0.00000667	1201
Loss of Function	1.73	26	37.4	0.695	0.00000203	416

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000065	rare
Latino/Admixed American	0.00070	0.00070	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00017	rare
South Asian	0.00017	0.00013	rare
Other	0.00099	0.00099	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.891
RVIS EVS: 0.69
RVIS percentile EVS: 85.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.317

Gene Damage Prediction

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