PWWP2A

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

Basic information

Region (hg38): 5:160061800-160119450

Links

ENSG00000170234 ∙ NCBI:114825 ∙ OMIM:617823 ∙ HGNC:29406 ∙ Uniprot:Q96N64 ∙ 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 PWWP2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PWWP2A 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	2	3
missense			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	2

Variants in PWWP2A

This is a list of pathogenic ClinVar variants found in the PWWP2A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160064958-G-A		not specified	Uncertain significance (May 11, 2022)
5-160064970-T-G		Abnormal brain morphology	Likely pathogenic (-)
5-160064999-C-G		not specified	Uncertain significance (Jan 12, 2024)
5-160080741-T-G		not specified	Uncertain significance (Jul 20, 2021)
5-160092418-G-A			Likely benign (Jan 01, 2023)
5-160092461-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-160092660-A-G		not specified	Uncertain significance (May 27, 2022)
5-160092729-T-G		not specified	Uncertain significance (Jan 23, 2023)
5-160092741-C-T		not specified	Likely benign (Mar 28, 2023)
5-160092743-T-C		not specified	Uncertain significance (May 08, 2024)
5-160092770-T-C		not specified	Uncertain significance (Jan 18, 2023)
5-160092772-C-G		not specified	Uncertain significance (Jun 23, 2021)
5-160092809-G-C		not specified	Uncertain significance (Jul 11, 2023)
5-160092926-G-T		not specified	Uncertain significance (Mar 06, 2023)
5-160092946-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-160092949-A-G			Benign (Oct 09, 2017)
5-160093006-A-C		not specified	Likely benign (Dec 06, 2023)
5-160093035-C-G		not specified	Uncertain significance (Mar 28, 2024)
5-160093077-T-C		not specified	Uncertain significance (Nov 06, 2023)
5-160093106-G-A		not specified	Uncertain significance (Jun 17, 2024)
5-160093167-C-T		not specified	Uncertain significance (Jan 23, 2024)
5-160093175-G-A		not specified	Uncertain significance (Dec 19, 2023)
5-160093268-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-160093298-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-160093389-T-C		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PWWP2A	protein_coding	protein_coding	ENST00000307063	2	57623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0171	124632	0	4	124636	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	268	400	0.670	0.0000210	4873
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000936
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000101	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.688
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.663

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pwwp2a

Gene ontology

• Cellular component: nucleus
• Molecular function: chromatin binding;protein binding;histone binding