HACE1
protein-codingHECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1, the group of HECT domain containing|Ankyrin repeat domain containing
Gene summary
This gene encodes a HECT domain and ankyrin repeat-containing ubiquitin ligase. The encoded protein is involved in specific tagging of target proteins, leading to their subcellular localization or proteasomal degradation. The protein is a potential tumor suppressor and is involved in the pathophysiology of several tumors, including Wilm's tumor. [provided by RefSeq, Mar 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~131.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014764
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014764
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014764
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014764
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HACE1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020771.4. 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 | 3 | 87 | 3 | 93 | ||
| missense | 1 | 2 | 120 | 4 | 1 | 128 |
| nonsense | 13 | 4 | 17 | |||
| start loss | 1 | 1 | ||||
| frameshift | 7 | 5 | 12 | |||
| splice donor/acceptor (+/-2bp) | 10 | 5 | 15 | |||
| Total | 21 | 21 | 129 | 91 | 4 | 266 |
Highest pathogenic variant AF is 0.000018720359
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065822.2 | 24 | MANE Select | |
| Ensembl | ENSP00000262903.4 | 24 | MANE Select | |
| RefSeq | NP_001308009.1 | 23 | Standard | |
| RefSeq | NP_001308012.1 | 23 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| hace1 | Danio rerio | Structure: atrioventricular canal Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Immune System
- Adaptive Immune System
- Antigen processing: Ubiquitination & Proteasome degradation
- Class I MHC mediated antigen processing & presentation
Biological Process
- protein polyubiquitination
- ubiquitin-dependent protein catabolic process
- Golgi organization
- cell cycle
- protein ubiquitination
Molecular Function
- ubiquitin-protein transferase activity
- protein binding
- Rab GTPase binding
- Rac GTPase binding
- ubiquitin protein ligase activity
Cellular Component
- Golgi membrane
- nucleus
- cytoplasm
- endoplasmic reticulum
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262903
- Coding exons
- 24
- Length
- 131827
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 125748
- p
- 0.000187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.59 | 259 | 481 | 0.539 | 0.0000240 | 6004 |
| Missense (PolyPhen) | 64 | 162.29 | 0.39435 | 2056 | ||
| Synonymous | -0.475 | 175 | 167 | 1.05 | 0.00000835 | 1681 |
| Loss of Function | 4.35 | 19 | 53.2 | 0.357 | 0.00000268 | 631 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase involved in Golgi membrane fusion and regulation of small GTPases. Acts as a regulator of Golgi membrane dynamics during the cell cycle: recruited to Golgi membrane by Rab proteins and regulates postmitotic Golgi membrane fusion. Acts by mediating ubiquitination during mitotic Golgi disassembly, ubiquitination serving as a signal for Golgi reassembly later, after cell division. Specifically interacts with GTP-bound RAC1, mediating ubiquitination and subsequent degradation of active RAC1, thereby playing a role in host defense against pathogens. May also act as a transcription regulator via its interaction with RARB. {ECO:0000269|PubMed:15254018, ECO:0000269|PubMed:21988917, ECO:0000269|PubMed:22036506}.;
- Disease
- DISEASE: Note=Defects in HACE1 are a cause of Wilms tumor (WT). WT is a pediatric malignancy of kidney and one of the most common solid cancers in childhood. HACE1 is epigenetically down-regulated in sporadic Wilms tumor. Moreover, a t(5;6)(q21;q21) translocation that truncates HACE1 has been found in a child with bilateral, young-onset Wilms tumor (PubMed:19948536). {ECO:0000269|PubMed:17694067, ECO:0000269|PubMed:19948536}.; DISEASE: Spastic paraplegia and psychomotor retardation with or without seizures (SPPRS) [MIM:616756]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPPRS is an autosomal recessive neurodevelopmental disorder manifesting in infancy. Affected individuals show hypotonia and psychomotor retardation. Most develop seizures. {ECO:0000269|PubMed:26424145, ECO:0000269|PubMed:26437029}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.680
- RVIS EVS
- -0.91
- RVIS percentile EVS
- 9.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.267
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |