WASF1
WASP family member 1, the group of Wiskott-Aldrich Syndrome protein family|A-kinase anchoring proteins|SCAR/WAVE complex
Basic information
Region (hg38): 6:110099819-110180004
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with absent language and variable seizures (Moderate), mode of inheritance: AD
- neurodevelopmental disorder with absent language and variable seizures (Strong), mode of inheritance: AD
- neurodevelopmental disorder with absent language and variable seizures (Moderate), mode of inheritance: AD
- neurodevelopmental disorder (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurodevelopmental disorder with absent language and variable seizures | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 29961568 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (44 variants)
- Inborn_genetic_diseases (40 variants)
- Neurodevelopmental_disorder_with_absent_language_and_variable_seizures (20 variants)
- WASF1-related_disorder (14 variants)
- Intellectual_disability (5 variants)
- not_specified (4 variants)
- Epileptic_encephalopathy (1 variants)
- Hereditary_ataxia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WASF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003931.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | |||||
| missense | 78 | 13 | 94 | |||
| nonsense | 6 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 4 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 7 | 3 | 82 | 20 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WASF1 | protein_coding | protein_coding | ENST00000392589 | 8 | 80186 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00243 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.55 | 175 | 299 | 0.586 | 0.0000158 | 3582 |
| Missense in Polyphen | 14 | 44.693 | 0.31325 | 504 | ||
| Synonymous | 1.32 | 88 | 105 | 0.836 | 0.00000545 | 1186 |
| Loss of Function | 4.15 | 1 | 22.1 | 0.0453 | 0.00000126 | 267 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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 (By similarity). As component of the WAVE1 complex, required for BDNF- NTRK2 endocytic trafficking and signaling from early endosomes (By similarity). {ECO:0000250|UniProtKB:Q8R5H6, ECO:0000269|PubMed:9889097}.;
- 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);VEGFA-VEGFR2 Signaling Pathway;Regulation of Actin Cytoskeleton;Signal Transduction;how does salmonella hijack a cell;VEGFA-VEGFR2 Pathway;rac1 cell motility signaling 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;RAC1 signaling pathway;E2F transcription factor network
(Consensus)
Intolerance Scores
- loftool
- 0.317
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.01
Haploinsufficiency Scores
- pHI
- 0.680
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.562
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.923
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wasf1
- Phenotype
- digestive/alimentary 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; muscle phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- receptor-mediated endocytosis;Rac protein signal transduction;actin filament polymerization;positive regulation of neurotrophin TRK receptor signaling pathway;protein-containing complex assembly;lamellipodium morphogenesis;dendrite extension;modification of postsynaptic actin cytoskeleton;dendritic transport of mitochondrion;cellular response to brain-derived neurotrophic factor stimulus;positive regulation of Arp2/3 complex-mediated actin nucleation
- Cellular component
- mitochondrial outer membrane;cytoskeleton;focal adhesion;actin cytoskeleton;lamellipodium;SCAR complex;dendrite cytoplasm;protein-containing complex;postsynapse
- Molecular function
- actin binding;protein binding;Rac GTPase binding;protein kinase A binding