WASHC3
protein-codingWASH complex subunit 3, the group of WASH complex
Gene summary
Predicted to be involved in actin filament polymerization and exocytosis. Part of WASH complex. [provided by Alliance of Genome Resources, Jul 2025]
- CCDC53
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to WASHC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016053.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 21 | 1 | 22 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 23 | 1 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057137.1 | 7 | MANE Select | |
| Ensembl | ENSP00000240079.6 | 7 | MANE Select | |
| RefSeq | NP_001288036.1 | 7 | Standard | |
| Ensembl | ENSP00000445501.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocytosis - Homo sapiens (human)
Biological Process
- exocytosis
- biological_process
- protein transport
- actin filament polymerization
Molecular Function
- protein binding
Cellular Component
- early endosome
- WASH complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000240079
- Coding exons
- 7
- Length
- 49223
- Individuals with no LoFs
- 124610
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 124636
- p
- 0.000104
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.433 | 80 | 91.7 | 0.873 | 0.00000431 | 1245 |
| Missense (PolyPhen) | 24 | 30.502 | 0.78683 | 430 | ||
| Synonymous | -1.53 | 41 | 30.3 | 1.35 | 0.00000142 | 371 |
| Loss of Function | 1.36 | 5 | 9.52 | 0.525 | 4.03e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00020 | 0.00019 | rare |
| Latino/Admixed American | 0.00010 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000061 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00016 | 0.00015 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts at least in part as component of the WASH core complex whose assembly at the surface of endosomes seems to inhibit WASH nucleation-promoting factor (NPF) activity in recruiting and activating the Arp2/3 complex to induce actin polymerization, and which is involved in regulation of the fission of tubules that serve as transport intermediates during endosome sorting (PubMed:19922875, PubMed:20498093). {ECO:0000269|PubMed:19922875, ECO:0000269|PubMed:20498093}.;
Intolerance Scores
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.28
Essentials
- Essential (gene trap)
- N