WIPF1

WAS/WASL interacting protein family member 1

Basic information

Region (hg38): 2:174559571-174682916

Previous symbols: [ "WASPIP" ]

Links

ENSG00000115935 ∙ NCBI:7456 ∙ OMIM:602357 ∙ HGNC:12736 ∙ Uniprot:O43516 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Wiskott-Aldrich syndrome 2 (Moderate), mode of inheritance: AR
• Wiskott-Aldrich syndrome 2 (Strong), mode of inheritance: AR
• Wiskott-Aldrich syndrome (Supportive), mode of inheritance: AD
• Wiskott-Aldrich syndrome 2 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Wiskott-Aldrich syndrome 2	AR	Allergy/Immunology/Infectious; Hematologic	Individuals have been described with frequent and severe infections (including a lethal infectious course in one individual), and thus, antiinfectious prophylaxis and early and aggressive treatment of infections and bleeding issues may be beneficial; Unrelated CBT has been reported as effective	Allergy/Immunology/Infectious; Dermatologic; Hematologic	22231303

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WIPF1 gene.

• Wiskott-Aldrich syndrome 2 (228 variants)
• not provided (23 variants)
• Inborn genetic diseases (20 variants)
• not specified (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WIPF1 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				67	8	75
missense			122	10	1	133
nonsense			1			1
start loss						0
frameshift						0
inframe indel			4	1		5
splice donor/acceptor (+/-2bp)						0
splice region			2	3	1	6
non coding			1	14	10	25
Total	0	0	128	92	19

Variants in WIPF1

This is a list of pathogenic ClinVar variants found in the WIPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-174562553-C-T		Wiskott-Aldrich syndrome 2	Likely benign (Aug 10, 2023)
2-174562554-G-A		Wiskott-Aldrich syndrome 2	Uncertain significance (Jul 28, 2022)
2-174562562-A-T		Wiskott-Aldrich syndrome 2	Likely benign (Apr 02, 2019)
2-174562578-C-T		Wiskott-Aldrich syndrome 2	Uncertain significance (Jan 31, 2020)
2-174562591-G-A		Wiskott-Aldrich syndrome 2	Uncertain significance (Aug 18, 2021)
2-174562602-C-T		Wiskott-Aldrich syndrome 2	Uncertain significance (Jan 02, 2024)
2-174562615-A-G		Wiskott-Aldrich syndrome 2	Likely benign (May 22, 2023)
2-174562616-C-T		Wiskott-Aldrich syndrome 2	Likely benign (Jan 01, 2024)
2-174566979-C-G		not specified	Benign (Jan 24, 2024)
2-174567061-A-G		Wiskott-Aldrich syndrome 2	Likely benign (Sep 23, 2022)
2-174567072-C-T		Wiskott-Aldrich syndrome 2	Uncertain significance (Aug 27, 2021)
2-174567073-G-A		Wiskott-Aldrich syndrome 2	Uncertain significance (Feb 09, 2022)
2-174567080-G-A		not specified • Wiskott-Aldrich syndrome 2	Benign/Likely benign (Feb 01, 2024)
2-174567085-T-C		Wiskott-Aldrich syndrome 2	Uncertain significance (Nov 16, 2019)
2-174567091-G-C		Wiskott-Aldrich syndrome 2	Uncertain significance (Mar 26, 2022)
2-174567100-G-T		Wiskott-Aldrich syndrome 2	Uncertain significance (Nov 01, 2022)
2-174567113-C-T		Wiskott-Aldrich syndrome 2	Benign (Jan 25, 2024)
2-174567114-G-A		Wiskott-Aldrich syndrome 2	Uncertain significance (May 26, 2022)
2-174567146-G-A		Wiskott-Aldrich syndrome 2	Conflicting classifications of pathogenicity (Dec 11, 2023)
2-174567152-C-T		Wiskott-Aldrich syndrome 2	Likely benign (Jan 15, 2020)
2-174567153-G-A		Wiskott-Aldrich syndrome 2	Uncertain significance (Aug 19, 2022)
2-174567162-T-C		Wiskott-Aldrich syndrome 2	Uncertain significance (Aug 19, 2022)
2-174567165-A-T		Wiskott-Aldrich syndrome 2	Uncertain significance (Nov 28, 2023)
2-174567188-G-A		Wiskott-Aldrich syndrome 2	Likely benign (Jul 29, 2023)
2-174567197-C-G		Wiskott-Aldrich syndrome 2	Likely benign (Oct 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WIPF1	protein_coding	protein_coding	ENST00000392547	7	123345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.903	0.0970	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	259	317	0.818	0.0000189	3155
Missense in Polyphen		117	164.78	0.71002		1584
Synonymous	0.560	127	135	0.939	0.00000935	1185
Loss of Function	3.29	2	16.3	0.122	9.46e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000265	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the reorganization of the actin cytoskeleton. Contributes with NCK1 and GRB2 in the recruitment and activation of WASL. May participate in regulating the subcellular localization of WASL, resulting in the disassembly of stress fibers in favor of filopodia formation. Plays a role in the formation of cell ruffles (By similarity). Plays an important role in the intracellular motility of vaccinia virus by functioning as an adapter for recruiting WASL to vaccinia virus. {ECO:0000250, ECO:0000269|PubMed:10878810, ECO:0000269|PubMed:19910490, ECO:0000269|PubMed:9405671}.
• Disease: DISEASE: Wiskott-Aldrich syndrome 2 (WAS2) [MIM:614493]: An immunodeficiency disorder characterized by eczema, thrombocytopenia, recurrent infections, defective T-cell proliferation, and impaired natural killer cell function. {ECO:0000269|PubMed:22231303}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Endocytosis - Homo sapiens (human);Signal Transduction;Fcgamma receptor (FCGR) dependent phagocytosis;TCR;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;KitReceptor;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of actin dynamics for phagocytic cup formation;Fc-epsilon receptor I signaling in mast cells (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.145
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.718
• hipred: Y
• hipred_score: 0.825
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wipf1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: actin cortical patch assembly;endocytosis;actin polymerization or depolymerization;actin filament-based movement;Fc-gamma receptor signaling pathway involved in phagocytosis;positive regulation of actin nucleation;actin cortical patch localization;response to other organism;protein-containing complex assembly
• Cellular component: ruffle;cytosol;actin filament;actin cytoskeleton;actin cortical patch;cytoplasmic vesicle
• Molecular function: actin binding;protein binding;profilin binding;SH3 domain binding;actin filament binding