PWWP3A

protein-coding

PWWP domain containing 3A, DNA repair factor, the group of PWWP domain containing

Gene summary

Enables nucleosome binding activity. Involved in DNA repair and chromatin organization. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MUM1

MANE transcript

NM_001369789.1

Inheritance

—

ClinVar variants

U:143B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr19:1,354,711-1,378,431

External References & Databases

Ensembl (ENSG00000160953)

Transcript & Mutation Effects

hg38 • Region Span ~23.7 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 PWWP3A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001369789.1. 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	2 clinvar	1 clinvar	4
missense			139 clinvar	15 clinvar		154
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	143	17	1	161

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001369789.1	RefSeq	NP_001356718.1	13	MANE Select
ENST00000591337.7	Ensembl	ENSP00000467287.4	13	MANE Select
NM_001369790.1	RefSeq	NP_001356719.1	14	Standard
NM_001369792.1	RefSeq	NP_001356721.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA repair
chromatin organization

Molecular Function

protein binding
nucleosome binding

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344663
Coding exons: 13
Length: 92541
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.330	391	410	0.954	0.0000259	4533
Missense (PolyPhen)		67	97.796	0.6851		1029
Synonymous	-1.06	198	180	1.10	0.0000130	1421
Loss of Function	3.62	11	33.6	0.327	0.00000177	401

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the DNA damage response pathway by contributing to the maintenance of chromatin architecture. Recruited to the vicinity of DNA breaks by TP53BP1 and plays an accessory role to facilitate damage-induced chromatin changes and promoting chromatin relaxation. Required for efficient DNA repair and cell survival following DNA damage. {ECO:0000269|PubMed:20347427}.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.542
RVIS EVS: -0.66
RVIS percentile EVS: 16.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0826

Gene Damage Prediction

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