HEXB

protein-coding

hexosaminidase 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

NM_000521.4

Inheritance

AR

ClinVar variants

P:254U:214B:228

Top phenotype

Sandhoff disease

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr5:74,640,023-74,722,647

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~82.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Sandhoff diseaseDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: G2P

Sandhoff diseaseDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: Ambry Genetics

Sandhoff diseaseDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: Natera

Sandhoff diseaseSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: Labcorp Genetics (formerly Invitae)

Sandhoff diseaseSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: Genomics England PanelApp

Sandhoff diseaseSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: PanelApp Australia

Sandhoff diseaseDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010006

Submitter: Myriad Women's Health

Sandhoff diseaseDEFINITIVE

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)

Sandhoff diseaseAR

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

Refs: 5651108; 571983; 3017984; 2948136; 8357844; 15956171; 18758829; 19898952; 20798201; 21150067; 22789865; 22848519; 23046579; 23113155Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HEXB variants in ClinVar

14 Conditions Cataloged
Sandhoff diseaseTotal: 829
not providedTotal: 106
Inborn genetic diseasesTotal: 78
not specifiedTotal: 53
HEXB-related disorderTotal: 17
HEXB-related disordersTotal: 7
Sandhoff disease, infantile formTotal: 4
Sandhoff disease, juvenile formTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
11
clinvar
212
clinvar
224
missense
5
clinvar
34
clinvar
194
clinvar
14
clinvar
1
clinvar
248
nonsense
24
clinvar
27
clinvar
1
clinvar
52
start loss
1
clinvar
1
frameshift
81
clinvar
54
clinvar
2
clinvar
137
splice donor/acceptor (+/-2bp)
5
clinvar
23
clinvar
5
clinvar
1
clinvar
34
Total1151392142271696

Highest pathogenic variant AF is 0.000776943

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000521.4RefSeqNP_000512.214MANE Select
ENST00000261416.12EnsemblENSP00000261416.714MANE Select
NM_001292004.2RefSeqNP_001278933.19Standard
ENST00000503312.5EnsemblENSP00000426384.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
hexbDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6482602910.8930.00001423609
Missense (PolyPhen)7390.8060.803911109
Synonymous-0.2581111081.030.000005151060
Loss of Function1.932031.70.6300.00000165368

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000870.00087rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish0.0000960.000092rare
European (Non-Finnish)0.000260.00025rare
South Asian0.000520.00052rare
Other0.000660.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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