PWWP2A

protein-coding

PWWP domain containing 2A, the group of PWWP domain containing

Gene summary

Enables several functions, including NuRD complex binding activity; histone H3K36me3 reader activity; and histone binding activity. Involved in chromatin remodeling. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001130864.2

Inheritance

—

ClinVar variants

U:91B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr5:160,061,801-160,119,450

External References & Databases

Ensembl (ENSG00000170234)

Transcript & Mutation Effects

hg38 • Region Span ~57.6 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 PWWP2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130864.2. 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	2 clinvar	4
missense			90 clinvar	3 clinvar		93
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	91	5	2	98

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130864.2	RefSeq	NP_001124336.1	2	MANE Select
ENST00000307063.9	Ensembl	ENSP00000305151.7	2	MANE Select
NM_001267035.3	RefSeq	NP_001253964.1	3	Standard
NM_001349732.2	RefSeq	NP_001336661.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

chromatin binding
protein binding
histone binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307063
Coding exons: 2
Length: 57623
Individuals with no LoFs: 124632
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 124636
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.35	268	400	0.670	0.0000210	4873
Missense (PolyPhen)		53	118.56	0.44702		1382
Synonymous	1.01	137	153	0.896	0.00000771	1560
Loss of Function	3.86	2	21.2	0.0943	0.00000134	270

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000010	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. Also required for proper mitosis progression. {ECO:0000269|PubMed:28645917}.;

Intolerance Scores

LoFtool: 0.334
RVIS EVS: 0
RVIS percentile EVS: 53.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.663

Gene Damage Prediction

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