WIPF3

WAS/WASL interacting protein family member 3

Basic information

Region (hg38): 7:29806485-29917061

Links

ENSG00000122574 ∙ NCBI:644150 ∙ OMIM:612432 ∙ HGNC:22004 ∙ Uniprot:A6NGB9 ∙ 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 WIPF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WIPF3 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
missense			39	2	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	2

Variants in WIPF3

This is a list of pathogenic ClinVar variants found in the WIPF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-29834729-C-T		not specified	Uncertain significance (Jan 04, 2024)
7-29834747-C-T		not specified	Uncertain significance (Mar 28, 2024)
7-29875876-G-A		not specified	Uncertain significance (Sep 22, 2023)
7-29875897-T-C		not specified	Uncertain significance (May 14, 2024)
7-29875906-G-A		not specified	Uncertain significance (Sep 14, 2022)
7-29875941-C-T		not specified	Uncertain significance (Aug 17, 2022)
7-29879028-A-T		not specified	Uncertain significance (May 23, 2023)
7-29879044-G-A		not specified	Uncertain significance (May 09, 2024)
7-29879117-C-G		not specified	Uncertain significance (Apr 01, 2024)
7-29879135-T-C		not specified	Likely benign (Sep 16, 2022)
7-29883879-C-G		not specified	Uncertain significance (Jan 10, 2023)
7-29883904-A-G		not specified	Uncertain significance (Oct 06, 2022)
7-29883917-C-G		not specified	Uncertain significance (Jul 27, 2022)
7-29884026-A-T		not specified	Uncertain significance (Nov 30, 2022)
7-29884030-C-T		not specified	Uncertain significance (Jun 11, 2024)
7-29884045-C-T		not specified	Uncertain significance (May 01, 2023)
7-29884080-A-G		not specified	Uncertain significance (Sep 26, 2023)
7-29884101-C-T		not specified	Uncertain significance (Apr 13, 2023)
7-29884126-A-C		not specified	Uncertain significance (Apr 27, 2023)
7-29884126-A-G		not specified	Uncertain significance (Mar 28, 2024)
7-29884129-T-C		not specified	Likely benign (Apr 13, 2022)
7-29884140-G-A		not specified	Uncertain significance (Sep 29, 2023)
7-29884141-C-T		not specified	Uncertain significance (Dec 27, 2023)
7-29884143-C-A		not specified	Uncertain significance (Dec 21, 2023)
7-29884143-C-T		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WIPF3	protein_coding	protein_coding	ENST00000409290	8	110581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00235	0.983	124585	0	54	124639	0.000217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.331	272	257	1.06	0.0000150	2944
Missense in Polyphen		56	57.875	0.9676		559
Synonymous	-0.624	120	112	1.08	0.00000716	1080
Loss of Function	2.13	7	16.3	0.430	9.64e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000308	0.000298
East Asian	0.0000556	0.0000556
Finnish	0.00143	0.00139
European (Non-Finnish)	0.000116	0.000115
Middle Eastern	0.0000556	0.0000556
South Asian	0.000177	0.000163
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a regulator of cytoskeletal organization. May have a role in spermatogenesis (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human);Signal Transduction;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of actin dynamics for phagocytic cup formation (Consensus)

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.144
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wipf3
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: actin cortical patch assembly;endocytosis;multicellular organism development;spermatogenesis;actin filament-based movement;cell differentiation;Fc-gamma receptor signaling pathway involved in phagocytosis;positive regulation of actin nucleation;actin cortical patch localization
• Cellular component: cytosol;actin filament;actin cortical patch
• Molecular function: SH3 domain binding;actin filament binding