WASF3

WASP family member 3, the group of Wiskott-Aldrich Syndrome protein family

Basic information

Region (hg38): 13:26557683-26688948

Links

ENSG00000132970 ∙ NCBI:10810 ∙ OMIM:605068 ∙ HGNC:12734 ∙ Uniprot:Q9UPY6 ∙ 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 WASF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASF3 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			28	2	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	3	4

Variants in WASF3

This is a list of pathogenic ClinVar variants found in the WASF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-26642314-G-A		not specified	Uncertain significance (Apr 12, 2024)
13-26642376-G-A		not specified	Uncertain significance (Apr 07, 2022)
13-26642379-A-G		not specified	Uncertain significance (Feb 28, 2024)
13-26642386-G-A		not specified	Uncertain significance (Nov 09, 2021)
13-26665018-T-C			Benign (Dec 31, 2019)
13-26665033-C-T		not specified	Uncertain significance (Oct 29, 2021)
13-26665063-A-G		not specified	Uncertain significance (May 09, 2022)
13-26665074-C-A		not specified	Uncertain significance (Sep 16, 2021)
13-26665117-C-T		not specified	Uncertain significance (May 07, 2024)
13-26665118-G-T		not specified	Uncertain significance (Jun 28, 2023)
13-26665127-T-C		not specified	Uncertain significance (Aug 03, 2022)
13-26665130-A-G		not specified	Uncertain significance (Feb 14, 2024)
13-26667593-C-G		not specified	Uncertain significance (Jun 24, 2022)
13-26667643-C-T		not specified	Uncertain significance (Apr 20, 2024)
13-26671945-C-G		not specified	Uncertain significance (Nov 21, 2022)
13-26676576-C-T		not specified	Uncertain significance (Nov 07, 2023)
13-26681059-A-G		not specified	Uncertain significance (Jan 09, 2024)
13-26681089-C-T		not specified	Uncertain significance (Jun 11, 2021)
13-26681163-G-A		not specified	Uncertain significance (Aug 26, 2022)
13-26681249-G-A			Likely benign (Jul 06, 2018)
13-26681254-C-G		not specified	Uncertain significance (Jul 20, 2022)
13-26681257-C-T		not specified	Uncertain significance (May 08, 2023)
13-26681265-C-G			Likely benign (Feb 01, 2023)
13-26681300-G-A			Benign (Dec 31, 2019)
13-26682660-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WASF3	protein_coding	protein_coding	ENST00000335327	8	131246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.540	0.460	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	257	322	0.798	0.0000198	3270
Missense in Polyphen		80	106.07	0.75422		1073
Synonymous	-0.300	135	131	1.03	0.00000928	1026
Loss of Function	3.27	4	19.6	0.204	8.97e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000615
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000808	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000670	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Downstream effector molecules involved in the transmission of signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape. {ECO:0000269|PubMed:17623672, ECO:0000269|PubMed:21834987}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Adherens junction - Homo sapiens (human);Signal Transduction;VEGFA-VEGFR2 Pathway;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;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.564
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.325
• hipred: Y
• hipred_score: 0.825
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wasf3

Gene ontology

• Biological process: cytoskeleton organization;regulation of cell shape;oligodendrocyte development;lamellipodium assembly;actin filament polymerization;positive regulation of myelination;protein-containing complex assembly;modification of postsynaptic actin cytoskeleton
• Cellular component: cytoplasm;cytoskeleton;lamellipodium;extracellular exosome;postsynapse;glutamatergic synapse
• Molecular function: actin binding