PWWP3A

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

Basic information

Region (hg38): 19:1354710-1378431

Previous symbols: [ "MUM1" ]

Links

ENSG00000160953 ∙ NCBI:84939 ∙ ∙ HGNC:29641 ∙ Uniprot:Q2TAK8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PWWP3A gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PWWP3A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			14	3		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	14	4	1

Variants in PWWP3A

This is a list of pathogenic ClinVar variants found in the PWWP3A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-1357078-C-G		not specified	Uncertain significance (Dec 03, 2021)
19-1358395-A-G		not specified	Uncertain significance (Jul 05, 2023)
19-1358417-T-C		not specified	Likely benign (Jan 30, 2024)
19-1358447-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-1360153-C-A		not specified	Uncertain significance (Feb 06, 2023)
19-1360157-C-T		not specified	Uncertain significance (Aug 02, 2023)
19-1360168-G-C		not specified	Uncertain significance (Sep 12, 2023)
19-1360187-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-1360195-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-1360210-G-A		not specified	Uncertain significance (May 09, 2022)
19-1360269-C-G		not specified	Uncertain significance (May 09, 2022)
19-1360270-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-1360304-C-T		not specified	Uncertain significance (Dec 11, 2023)
19-1360307-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-1360324-T-G		not specified	Uncertain significance (Dec 19, 2023)
19-1360337-C-T		not specified	Likely benign (Jun 23, 2023)
19-1360354-G-A		not specified	Uncertain significance (Jul 21, 2021)
19-1360397-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-1360487-C-T		not specified	Likely benign (Dec 28, 2023)
19-1360512-T-A			Likely benign (Dec 18, 2017)
19-1360513-G-T		not specified	Likely benign (Oct 06, 2023)
19-1360543-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-1360679-C-T		not specified	Likely benign (Sep 12, 2023)
19-1360744-C-T			Benign (Dec 18, 2017)
19-1360756-A-G		not specified	Likely benign (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PWWP3A	protein_coding	protein_coding	ENST00000344663	13	92541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00215	0.998	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	391	410	0.954	0.0000259	4533
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000608
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000223	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000223	0.000217
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0715
• hipred: N
• hipred_score: 0.309
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mum1

Gene ontology

• Biological process: DNA repair;chromatin organization
• Cellular component: nucleus;cytosol
• Molecular function: protein binding;nucleosome binding