HEXB
protein-codinghexosaminidase subunit beta, the group of Hexosaminidases
Gene summary
Hexosaminidase B is the beta subunit of the lysosomal enzyme beta-hexosaminidase that, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Beta-hexosaminidase is composed of two subunits, alpha and beta, which are encoded by separate genes. Both beta-hexosaminidase alpha and beta subunits are members of family 20 of glycosyl hydrolases. Mutations in the alpha or beta subunit genes lead to an accumulation of GM2 ganglioside in neurons and neurodegenerative disorders termed the GM2 gangliosidoses. Beta subunit gene mutations lead to Sandhoff disease (GM2-gangliosidosis type II). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0010006
Submitter: ClinGen
HEXB was first reported in relation to Sandhoff disease, an autosomal recessive lysosomal storage disorder, in 1986 (O’Dowd et al., PMID: 3017984). HEXB encodes the beta subunit of the enzyme hexosaminidase which is involved in the breakdown of GM2-gangliosides. A deficiency of Hex B results in reduced hexosaminidase activity, and subsequent accumulation of GM2-gangliosides in neuronal cells. Accumulation of GM2-gangliosides in neuronal cells causes various symptoms including developmental regression, exaggerated startle response, and a cherry-red spot on the macula. Sandhoff disease has a phenotypic continuum and can be divided into three clinical phenotypes: acute infantile, subacute juvenile, and late-onset SD. The diagnosis of Sandhoff disease is established by abnormally low enzymatic activity of hexosaminidases A and B, and identification of biallelic pathogenic variants in HEXB by molecular genetic testing (Xiao et al., 2022, PMID: 35420740). Six variants (1 missense, 1 splice site, 2 nonsense, 2 frameshift) that have been reported in five probands in two publications (Zampieri S, et al., 2009, PMID: 18758829; Alonso-Pérez J et al., 2021, PMID: 34210542) are included in this curation. Individuals with two null variants typically have the acute infantile phenotype, whereas individuals with one null and one missense variant typically have the subacute juvenile phenotype, and individuals with two missense variants typically have the late-onset phenotype (Xiao et al., 2022, PMID: 35420740). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity is loss of function. This gene-disease relationship is also supported by experimental evidence including animal models systems, rescue in animal models, protein interaction, and biochemical function of the HexB enzyme. Individuals with Sandhoff disease show accumulation of GM2 gangliosides in the neurons due to reduced or undetectable levels of hexosaminidase activity (Mahuran DJ, 1999, PMID: 10571007). The gene product of HEXB interacts with HEXA and GM2A which have both been implicated in other forms of GM2 gangliosidosis and exhibit symptoms similar to Sandhoff disease (Lemieux MJ, et al., 2006, PMID: 16698036). Zebrafish show loss of enzyme activity, accumulation of oligosaccharides, lysosomal abnormalities in glia and reduced locomotor activity, similar to the molecular, cellular, neuropathological, and motility aspects of Sandhoff disease in humans. Hexb deficient zebrafish seem to recapitulate early disease stages, but lack extensive neurodegeneration (Kuil LE et al., 2019, PMID: 31140649). Knockout mouse models displayed biochemical and clinical features similar to those seen in humans with Sandhoff disease (Phaneuf D, et al., 1996, PMID: 8789434; Sango K, et al., 1995, PMID: 7550345) Gene therapy in mice partially restored hexb activity in the brain, which had the following effects: normalized lysosomal function, corrected lipid storage, prevented GM2 storage, prevented neuroinflammation, and restored a normal lifespan and locomotor function (Niemir N, et al., 2018, PMID: 29325092; Dogbevia G, et al., 2020, PMID: 31357902). In summary, HEXB is definitively associated with Sandhoff disease. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Lysosomal Diseases Gene Curation Expert Panel on the meeting date 9/15/2022 (SOP Version 9).
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Neurologic; Ophthalmologic
Intervention: General
Rationale: Substrate reduction therapy has been described as potentially beneficial; 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 HEXB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000521.4. 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 | 1 | 11 | 212 | 224 | ||
| missense | 5 | 34 | 194 | 14 | 1 | 248 |
| nonsense | 24 | 27 | 1 | 52 | ||
| start loss | 1 | 1 | ||||
| frameshift | 81 | 54 | 2 | 137 | ||
| splice donor/acceptor (+/-2bp) | 5 | 23 | 5 | 1 | 34 | |
| Total | 115 | 139 | 214 | 227 | 1 | 696 |
Highest pathogenic variant AF is 0.000776943
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000512.2 | 14 | MANE Select | |
| Ensembl | ENSP00000261416.7 | 14 | MANE Select | |
| RefSeq | NP_001278933.1 | 9 | Standard | |
| Ensembl | ENSP00000426384.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| hexb | Danio rerio | Structure: intersegmental vessel Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
- Lysosome - Homo sapiens (human)
- Other glycan degradation - Homo sapiens (human)
- Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
- Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
Biological Process
- skeletal system development
- glycosphingolipid metabolic process
- ganglioside catabolic process
- cellular calcium ion homeostasis
- lysosome organization
Molecular Function
- beta-N-acetylhexosaminidase activity
- protein binding
- acetylglucosaminyltransferase activity
- protein homodimerization activity
- protein heterodimerization activity
Cellular Component
- acrosomal vesicle
- extracellular region
- membrane
- azurophil granule lumen
- azurophil granule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000261416
- Coding exons
- 14
- Length
- 82625
- Individuals with no LoFs
- 125661
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 87
- Defined
- 125748
- p
- 0.000346
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.648 | 260 | 291 | 0.893 | 0.0000142 | 3609 |
| Missense (PolyPhen) | 73 | 90.806 | 0.80391 | 1109 | ||
| Synonymous | -0.258 | 111 | 108 | 1.03 | 0.00000515 | 1060 |
| Loss of Function | 1.93 | 20 | 31.7 | 0.630 | 0.00000165 | 368 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00087 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000096 | 0.000092 | rare |
| European (Non-Finnish) | 0.00026 | 0.00025 | rare |
| South Asian | 0.00052 | 0.00052 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Responsible for the degradation of GM2 gangliosides, and a variety of other molecules containing terminal N-acetyl hexosamines, in the brain and other tissues.;
- Disease
- DISEASE: GM2-gangliosidosis 2 (GM2G2) [MIM:268800]: An autosomal recessive lysosomal storage disease marked by the accumulation of GM2 gangliosides in the neuronal cells. Clinically indistinguishable from GM2-gangliosidosis type 1, presenting startle reactions, early blindness, progressive motor and mental deterioration, macrocephaly and cherry-red spots on the macula. {ECO:0000269|PubMed:1531140, ECO:0000269|PubMed:1720305, ECO:0000269|PubMed:7557963, ECO:0000269|PubMed:7626071, ECO:0000269|PubMed:7633435, ECO:0000269|PubMed:8357844, ECO:0000269|PubMed:8950198, ECO:0000269|PubMed:9401004, ECO:0000269|PubMed:9694901, ECO:0000269|PubMed:9856491}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0805
Intolerance Scores
- LoFtool
- 0.371
- RVIS EVS
- 0.95
- RVIS percentile EVS
- 90.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.667
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |