HACE1

protein-coding

HECT 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

NM_020771.4

Inheritance

AR

ClinVar variants

P:42U:129B:95

Top phenotype

Spastic paraplegia and psychomotor retardation with or without seizures

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr6:104,728,094-104,859,919

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~131.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spastic paraplegia-severe developmental delay-epilepsy syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014764

Submitter: Orphanet

spastic paraplegia-severe developmental delay-epilepsy syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014764

Submitter: G2P

spastic paraplegia-severe developmental delay-epilepsy syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014764

Submitter: Labcorp Genetics (formerly Invitae)

spastic paraplegia-severe developmental delay-epilepsy syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014764

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Spastic paraplegia and psychomotor retardation with or without seizuresAR

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

Refs: 26424145; 26437029Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HACE1 variants in ClinVar

13 Conditions Cataloged
not providedTotal: 237
Inborn genetic diseasesTotal: 62
Spastic paraplegia-severe developmental delay-epilepsy syndromeTotal: 50
not specifiedTotal: 27
HACE1-related disorderTotal: 16
HACE1-related disordersTotal: 1
HACE1-related neurodevelopmental disorderTotal: 1
Generalized hypotoniaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
87
clinvar
3
clinvar
93
missense
1
clinvar
2
clinvar
120
clinvar
4
clinvar
1
clinvar
128
nonsense
13
clinvar
4
clinvar
17
start loss
1
clinvar
1
frameshift
7
clinvar
5
clinvar
12
splice donor/acceptor (+/-2bp)
10
clinvar
5
clinvar
15
Total2121129914266

Highest pathogenic variant AF is 0.000018720359

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020771.4RefSeqNP_065822.224MANE Select
ENST00000262903.9EnsemblENSP00000262903.424MANE Select
NM_001321080.2RefSeqNP_001308009.123Standard
NM_001321083.2RefSeqNP_001308012.123Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
hace1Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.592594810.5390.00002406004
Missense (PolyPhen)64162.290.394352056
Synonymous-0.4751751671.050.000008351681
Loss of Function4.351953.20.3570.00000268631

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.000170.00017rare
Ashkenazi Jewish00.0absent
East Asian0.000380.00038rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000160.00016rare
South Asian0.000360.00036rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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