WASHC5
protein-codingWASH complex subunit 5, the group of WASH complex
Gene summary
This gene encodes a 134 kDa protein named strumpellin that is predicted to have multiple transmembrane domains and a spectrin-repeat-containing domain. This ubiquitously expressed gene has its highest expression in skeletal muscle. The protein is named for Strumpell disease; a form of hereditary spastic paraplegia (HSP). Spastic paraplegias are a diverse group of disorders in which the autosomal dominant forms are characterized by progressive, lower extremity spasticity caused by axonal degeneration in the terminal portions of the longest descending and ascending corticospinal tracts. More than 30 loci (SPG1-33) have been implicated in hereditary spastic paraplegia diseases. [provided by RefSeq, Aug 2009]
- SPG8
- KIAA0196
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~67.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0009073
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009073
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009073
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0019078
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009073
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0011339
Submitter: ClinGen
The WASHC5 gene is located on chromosome 8 at 8q24.13 and encodes the WASH complex subunit 5 protein, or strumpellin, a component of the WASH core complex, which activates Arp2/3-mediated actin polymerization and functions in endosome fission. WASHC5 was first reported in relation to autosomal dominant hereditary spastic paraplegia 8 in 2007 (Valdmanis et al., PMID: 17160902). This disorder is a slowly progressive, typically pure spastic paraplegia of the lower limbs characterized by pyramidal signs including hyperreflexia, extensor plantar reflexes, spasticity, and clonus without other neurological findings; mild distal decreased vibration sense; and urinary urgency that becomes apparent with spasticity. More complex phenotypic features may present, including ataxia, seizures, intellectual disability, dementia, muscle atrophy, extrapyramidal disturbance, and peripheral neuropathy. Onset is typically between 10 and 59 years of age and affected individuals often become wheelchair dependent. WASHC5 has also been associated with autosomal recessive Ritscher-Schinzel syndrome 1 by Elliott et al. in 2013 (PMID: 24065355). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, there is a difference in inheritance pattern and in clinical phenotype. Therefore, the diseases were split into hereditary spastic paraplegia 8 (OMIM: 603563) and Ritscher-Schinzel syndrome 1 (OMIM: 220210). The split curation for autosomal Ritscher-Schinzel syndrome 1 has been curated separately. Evidence supporting the relationship between WASHC5 and hereditary spastic paraplegia 8 includes case-level data and experimental data. Numerous unique variants have been reported in humans in multiple publications. While most reported variants are missense variants, putative loss-of-function variants are also identified in a small number of cases, including a small intragenic deletion (Ishiura et al., 2014, PMID: 24451228) Segregation of a variant with disease was demonstrated in several families (Valdmanis et al., 2007, PMID: 17160902). Additional variants were evaluated but not scored due to their presence at high frequency in public databases. The mechanism of disease has not yet been clearly established, but haploinsufficiency has been suggested (Clemen et al., 2010, PMID: 20833645). Small hairpin RNA-mediated strumpellin knockdown in human neuroblastoma cells showed a highly significant reduction of axonal outgrowth in the knockdown cells versus controls cells (Clemen et al. 2010; PMID: 20833645), while a knockdown zebrafish model recapitulated some aspects of the human phenotype (Valdmanis et al., 2007, PMID: 17160902). In summary, there is moderate evidence to support the association of WASHC5 with autosomal dominant hereditary spastic paraplegia 8. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Syndromic Disorders Gene Curation Expert Panel on the meeting date 09.17.2021 (SOP Version 8). This GDR was reevaluated on 30 September, 2024 (SOP Version 10). Although three new case reports were published, the classification did not change.
Inheritance Pattern: AD
Disease ID:MONDO:0011339
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009073
Submitter: ClinGen
The *WASHC5* gene is located on chromosome 8 at 8q24.13 and encodes the WASH complex subunit 5 protein, or strumpellin, a component of the WASH core complex, which activates Arp2/3-mediated actin polymerization and functions in endosome fission. *WASHC5* was first reported in relation to autosomal recessive Ritscher-Schinzel syndrome 1 in 2013 (Elliott et al., PMID: 24065355). This disorder is characterized by brain malformations, with neurodevelopmental findings, dysmorphic features, and cardiovascular malformations. *WASHC5* has also been associated with autosomal dominant hereditary spastic paraplegia 8 by Valdmanis et al. in 2007 (PMID: 17160902). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found a difference in inheritance pattern and in clinical phenotype between the two disease assertions. Therefore, the diseases were split into Ritscher-Schinzel syndrome 1 (OMIM: 220210) and hereditary spastic paraplegia 8 (OMIM: 603563). The split curation for autosomal recessive hereditary spastic paraplegia 8 has been curated separately. Evidence supporting the relationship between *WASHC5* and Ritscher-Schinzel syndrome 1 includes case-level data. Elliott et al. (2013, PMID: 24065355) identified a homozygous canonical splice site variant in 10 affected individuals from an isolated First Nations community. A homozygous missense variant was identified in another individual but was not scored (Maddirevula et al., 2020, PMID: 33456446). This gene-disease relationship is not supported by experimental evidence. There are two animal models (one mouse and one zebrafish) reported in the literature but neither provide evidence to support the gene-disease relationship (Bu et al., PMID:32417190) In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This gene-disease pair was originally evaluated by the ClinGen Syndromic Disorders GCEP on September 17, 2021. It was reevaluated on December 4, 2024 (SOP Version 11). Although a new case report was published (PMID: 36130690), the classification did not change.
Inheritance Pattern: AD
Disease ID:MONDO:0011339
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Neurologic; Ophthalmologic
Intervention: Cardiovascular
Rationale: The condition may involve congenital heart anomalies, some of which may require surgical and other interventions, and awareness may allow early diagnosis and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to WASHC5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014846.4. 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 | 12 | 116 | 1 | 129 | ||
| missense | 5 | 12 | 277 | 14 | 3 | 311 |
| nonsense | 5 | 9 | 6 | 1 | 21 | |
| start loss | 1 | 1 | ||||
| frameshift | 7 | 9 | 7 | 23 | ||
| splice donor/acceptor (+/-2bp) | 11 | 8 | 19 | |||
| Total | 17 | 41 | 311 | 131 | 4 | 504 |
Highest pathogenic variant AF is 0.000017969585
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055661.3 | 28 | MANE Select | |
| Ensembl | ENSP00000318016.7 | 28 | MANE Select | |
| RefSeq | NP_001317538.1 | 25 | Standard | |
| Ensembl | ENSP00000429676.1 | 25 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| washc5 | Danio rerio | Structure: motor neuron Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocytosis - Homo sapiens (human)
Biological Process
- oocyte maturation
- positive regulation of neuron projection development
- protein transport
- endosomal transport
- polar body extrusion after meiotic divisions
Molecular Function
- protein binding
Cellular Component
- nucleoplasm
- early endosome
- endoplasmic reticulum
- cytosol
- neuron projection
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000318410
- Coding exons
- 28
- Length
- 67581
- Individuals with no LoFs
- 125635
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 113
- Defined
- 125748
- p
- 0.000449
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.30 | 527 | 618 | 0.853 | 0.0000334 | 7654 |
| Missense (PolyPhen) | 188 | 239.56 | 0.78478 | 2978 | ||
| Synonymous | -0.464 | 235 | 226 | 1.04 | 0.0000127 | 2169 |
| Loss of Function | 3.29 | 39 | 68.3 | 0.571 | 0.00000372 | 790 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00056 | 0.00056 | rare |
| South Asian | 0.00042 | 0.00042 | rare |
| Other | 0.00049 | 0.00049 | 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). May be involved in axonal outgrowth. Involved in cellular localization of ADRB2 (PubMed:23085491). Involved in cellular trafficking of BLOC-1 complex cargos such as ATP7A and VAMP7 (PubMed:23676666). {ECO:0000269|PubMed:19922875, ECO:0000269|PubMed:20833645, ECO:0000269|PubMed:23085491, ECO:0000269|PubMed:23676666}.;
- Disease
- DISEASE: Ritscher-Schinzel syndrome 1 (RTSC1) [MIM:220210]: A developmental malformation syndrome characterized by craniofacial abnormalities, congenital heart defects, and cerebellar brain malformations. Facial features include prominent occiput, prominent forehead, low-set ears, downslanting palpebral fissures, depressed nasal bridge, and micrognathia. Cardiac defects can include septal defects and aortic stenosis, among others, and brain imaging shows Dandy-Walker malformation, cerebellar vermis hypoplasia, posterior fossa cysts, and ventricular dilatation. Affected individuals have severe developmental delay. {ECO:0000269|PubMed:24065355}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- RVIS EVS
- -1.3
- RVIS percentile EVS
- 4.93
Essentials
- Essential (gene trap)
- N