WASF2

WASP family member 2, the group of Wiskott-Aldrich Syndrome protein family

Basic information

Region (hg38): 1:27404230-27490167

Links

ENSG00000158195 ∙ NCBI:10163 ∙ OMIM:605875 ∙ HGNC:12733 ∙ Uniprot:Q9Y6W5 ∙ 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 WASF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASF2 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			24	2		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	24	3	0

Variants in WASF2

This is a list of pathogenic ClinVar variants found in the WASF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27408193-T-C		not specified	Uncertain significance (Jun 03, 2022)
1-27408229-T-A		not specified	Uncertain significance (Apr 23, 2024)
1-27408265-G-C		not specified	Uncertain significance (Feb 12, 2024)
1-27408335-G-A		not specified	Uncertain significance (Oct 17, 2023)
1-27409772-A-G		not specified	Uncertain significance (Jan 10, 2023)
1-27409775-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-27409832-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-27409840-A-G			Likely benign (Mar 28, 2018)
1-27409854-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-27409934-G-C		not specified	Uncertain significance (Jan 25, 2023)
1-27410034-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-27410054-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-27410090-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-27410103-G-T		not specified	Uncertain significance (Feb 11, 2022)
1-27412584-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-27412626-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-27412656-G-A			Likely benign (Apr 02, 2018)
1-27412665-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-27412705-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-27414962-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-27416079-T-C		not specified	Uncertain significance (Oct 04, 2022)
1-27418345-A-T		not specified	Uncertain significance (Apr 24, 2024)
1-27418350-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-27418375-T-C		not specified	Uncertain significance (Jun 28, 2022)
1-27418998-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WASF2	protein_coding	protein_coding	ENST00000430629	8	85940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0243	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	206	291	0.708	0.0000161	3220
Missense in Polyphen		21	34.554	0.60775		301
Synonymous	0.299	107	111	0.964	0.00000660	1058
Loss of Function	3.76	2	20.2	0.0988	0.00000108	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Downstream effector molecule involved in the transmission of signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. Promotes formation of actin filaments. Part of the WAVE complex that regulates lamellipodia formation. The WAVE complex regulates actin filament reorganization via its interaction with the Arp2/3 complex. {ECO:0000269|PubMed:10381382, ECO:0000269|PubMed:16275905}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Adherens junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Regulation of Actin Cytoskeleton;Signal Transduction;VEGFA-VEGFR2 Pathway;y branching of actin filaments;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;ErbB1 downstream signaling;Regulation of actin dynamics for phagocytic cup formation;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;RAC1 signaling pathway;PDGFR-beta signaling pathway;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.309
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.442
• hipred: Y
• hipred_score: 0.628
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wasf2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); embryo phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: angiogenesis;ameboidal-type cell migration;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;positive regulation of lamellipodium assembly;viral process;Rac protein signal transduction;lamellipodium assembly;actin cytoskeleton organization;actin filament-based movement;megakaryocyte development;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;negative regulation of stress fiber assembly;lamellipodium morphogenesis;postsynaptic actin cytoskeleton organization
• Cellular component: ruffle;early endosome;cytosol;cell-cell junction;actin cytoskeleton;lamellipodium;SCAR complex;protein-containing complex;synapse;extracellular exosome
• Molecular function: actin binding;protein binding;SH3 domain binding;cadherin binding;protein kinase A binding