EXT2

gene
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Also known as SOTV

Summary

EXT2 (exostosin glycosyltransferase 2, HGNC:3513) is a protein-coding gene on chromosome 11p11.2, encoding Exostosin-2 (Q93063). Glycosyltransferase forming with EXT1 the heterodimeric heparan sulfate polymerase which catalyzes the elongation of the heparan sulfate glycan backbone. It is a selective cancer dependency (DepMap: 12.9% of cell lines) and haploinsufficient (ClinGen: sufficient evidence).

This gene encodes one of two glycosyltransferases involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type II form of multiple exostoses. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.

Source: NCBI Gene 2132 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): exostoses, multiple, type 2 (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 3
  • Clinical variants (ClinVar): 1,033 total — 196 pathogenic, 41 likely-pathogenic
  • Phenotypes (HPO): 142
  • Cancer dependency (DepMap): dependent in 12.9% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_207122

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3513
Approved symbolEXT2
Nameexostosin glycosyltransferase 2
Location11p11.2
Locus typegene with protein product
StatusApproved
AliasesSOTV
Ensembl geneENSG00000151348
Ensembl biotypeprotein_coding
OMIM608210
Entrez2132

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 17 protein_coding, 6 retained_intron, 5 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined

ENST00000343631, ENST00000358681, ENST00000395673, ENST00000525559, ENST00000528159, ENST00000529186, ENST00000531161, ENST00000533608, ENST00000534048, ENST00000682359, ENST00000682711, ENST00000682815, ENST00000682947, ENST00000682993, ENST00000683000, ENST00000683204, ENST00000683299, ENST00000683870, ENST00000683881, ENST00000684039, ENST00000684124, ENST00000684437, ENST00000684533, ENST00000860016, ENST00000860017, ENST00000860018, ENST00000860019, ENST00000860020, ENST00000860021, ENST00000860022, ENST00000958404, ENST00000958405

RefSeq mRNA: 5 — MANE Select: NM_207122 NM_000401, NM_001178083, NM_001389628, NM_001389630, NM_207122

CCDS: CCDS53619, CCDS7908

Canonical transcript exons

ENST00000533608 — 14 exons

ExonStartEnd
ENSE000008245514419782944198018
ENSE000009990534412478944124984
ENSE000011013784423629344236375
ENSE000013244014409567844095852
ENSE000021762514424414944251962
ENSE000034778954417161144171742
ENSE000035058134420679344206959
ENSE000035191274411418544114301
ENSE000035254854413004544130138
ENSE000035453574410768344108248
ENSE000035569914423235344232496
ENSE000035581874410919444109283
ENSE000036465994423411544234243
ENSE000036636644412681644126955

Expression profiles

Bgee: expression breadth ubiquitous, 269 present calls, max score 97.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.8422 / max 315.0899, expressed in 1824 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
11398136.32651821
1139806.82191745
1139826.75901751
1139836.72481704
1139841.2100570

Top tissues by expression

284 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225597.35gold quality
cartilage tissueUBERON:000241894.92gold quality
smooth muscle tissueUBERON:000113594.87gold quality
tibiaUBERON:000097994.53gold quality
islet of LangerhansUBERON:000000694.21gold quality
body of uterusUBERON:000985393.53gold quality
thoracic aortaUBERON:000151593.49gold quality
ascending aortaUBERON:000149693.47gold quality
right coronary arteryUBERON:000162593.47gold quality
descending thoracic aortaUBERON:000234593.30gold quality
ventricular zoneUBERON:000305393.29gold quality
periodontal ligamentUBERON:000826693.15gold quality
left uterine tubeUBERON:000130392.87gold quality
left coronary arteryUBERON:000162692.60gold quality
endocervixUBERON:000045892.51gold quality
aortaUBERON:000094792.39gold quality
coronary arteryUBERON:000162192.23gold quality
gall bladderUBERON:000211092.15gold quality
pericardiumUBERON:000240792.11gold quality
myometriumUBERON:000129692.00gold quality
left ovaryUBERON:000211991.93gold quality
right ovaryUBERON:000211891.91gold quality
popliteal arteryUBERON:000225091.66gold quality
tibial arteryUBERON:000761091.66gold quality
placentaUBERON:000198791.59gold quality
ectocervixUBERON:001224991.56gold quality
peritoneumUBERON:000235891.52gold quality
omental fat padUBERON:001041491.52gold quality
deciduaUBERON:000245091.40gold quality
adipose tissue of abdominal regionUBERON:000780891.22gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting EXT2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-188-3P100.0068.761240
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-590-3P99.9674.346478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-4802-3P99.7270.131273
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-518A-5P99.7069.012209
HSA-MIR-52799.7069.012209
HSA-MIR-670-5P99.6769.941565
HSA-MIR-7156-5P99.6468.811369
HSA-MIR-4756-3P99.6266.301319
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-431099.5968.842527
HSA-MIR-4524A-5P99.5771.731193
HSA-MIR-4524B-5P99.5771.681195
HSA-MIR-4728-3P99.4768.94981
HSA-MIR-330-3P99.4169.952521
HSA-MIR-2116-5P99.3269.341273
HSA-MIR-6719-3P99.2967.781387
HSA-MIR-580-5P99.2870.941776
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-1207-3P98.9966.221532

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 12.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • the EXT1/2 heterocomplex can act as heparan sulfate polymerases in vitro without the addition of additional auxiliary proteins (PMID:12907669)
  • 112delAT causes multiple exostoses, indicating full penetrance since relatives with isolated exotoses lacked this deletion. (PMID:14654969)
  • Variations in EXT2 gene is associated with multiple osteochondromas (PMID:15586175)
  • Promoter methylation was not detected in any of the chondrosarcoma cases in EXT2. (PMID:15796962)
  • analysis of multiple osteochondroma-related mutations in EXT1 and EXT2 (PMID:16088908)
  • We found three novel mutations (S277X in the EXT1 gene, and G194X and 939+1G>A in the EXT2 gene) and a known mutation (Q172X in the EXT2 gene)in hereditary multiple exostoses (PMID:16638657)
  • Detection of mutations in EXT2 gene can significantly improve the identification of both point-mutations and mid-size rearrangemements in osteochrondromas. (PMID:17301954)
  • Hereditary multiple exostosis patients with mutations in EXT1 gene have more anatomic abnormality and burden than those with EXT2 mutations. (PMID:17589361)
  • Compared to EXT2-linkage, female individuals with EXT1-linkage were smaller in stature. (PMID:17676624)
  • capacity of wild type EXT2 to enhance heparan sulfate chain length together with EXT1 was not shared by the EXT2-Y419X mutant (PMID:17761672)
  • A novel mutation, c505 G > T, in the EXT2 gene was identified in two unrelated Chinese families with hereditary multiple exostoses. (PMID:18294062)
  • found EXT1 to be responsible in seven families (19 affected members) and EXT2 in four families (17 affected members) with multiple osteochondromas (PMID:18373409)
  • A novel mutation in EXT2 gene in a Chinese family with hereditary exostoses is reported. (PMID:18666861)
  • Data show that SNPs in EXT2 did not confer a significant risk for type 2 diabetes in Pima Indians. (PMID:19008344)
  • The tumor suppressor gene EXT2 is involved in the formation of multiple osteochondromas, which can progress to become secondary peripheral chondrosarcomas. (PMID:19179614)
  • A previously unreported stop mutation, the substitution c.817C>T, was observed in the EXT2 gene in an Indian pedigree of hereditary multiple exostoses families. (PMID:19309273)
  • Novel mutations have been identified in the EXT1 and the EXT2 gene in 17 Multiple Osteochondromas patients. (PMID:19344451)
  • Two novel EXT1 gene mutations and two novel EXT2 gene mutations were identified in two and three hereditary multiple exostoses pedigrees, respectively. (PMID:19839753)
  • The nonsens mutation 536G>A in the EXT2 is the disease-causing mutation in a family with hereditary multiple exostoses. (PMID:20140877)
  • results clearly indicate that, in most cases, biallelic inactivation of EXT genes does not account for osteochondromas formation; this mechanism should be regarded as a common feature for hereditary osteochondromas transformation (PMID:20418910)
  • Loss of heterozygosity for EXT2 is associated with multiple osteochondromas. (PMID:20813973)
  • primary defect in EXT2 mRNA level can produce profound effect on the synthesis of HS chains in cartilage, the consequence of which impacts on the regulation of chondrocyte proliferation and differentiation. (PMID:20872591)
  • 8 novel mutations of EXT1 and EXT2 genes among families and sporadic cases with multiple exostoses were identified. (PMID:21039224)
  • Fifteen mutations and large deletions, of which nine are new, were detected in the EXT1 and EXT2 gene by sequence analysis, FISH and MLPA analysis. (PMID:21499719)
  • Association of genetic variations in EXT2 with Type 2 diabetes mellitus in Tunisia (PMID:21510814)
  • Molecular characterization of EXT1- and EXT2-deletion breakpoints in multiple osteochondroma indicates that non-allelic homologous recombination between Alu-sequences as well as NHEJ are causal and that the majority of these deletions are nonrecurring. (PMID:21703028)
  • Two novel EXT1 gene mutations were identified and no mutation was found in EXT2 gene in two families with multiple osteochodromas. (PMID:22040554)
  • analysis of novel pathogenic mutations in EXT1 and EXT2 that may have roles in multiple osteochondroma in Chinese patients (PMID:22820392)
  • A meta analysis indicates variation in the EXT2 locus appears to be associated with a small increase in the risk of type 2 diabetes. (PMID:23052945)
  • 20 novel EXT1/EXT2 mutations and one large EXT2 deletion identified in the largest Southern Italy cohort of patients affected by hereditary multiple exostosis. (PMID:23262345)
  • we found a mutation in EXT1 or in EXT2 in 95% of the Spanish patients. Eighteen of the mutations were novel. (PMID:23439489)
  • No mutations have been found among all exons of the EXT1 and EXT2 genes in this family. Linkage analysis is necessary for identifying the cause of this disease. (PMID:23450490)
  • Novel and recurrent mutations occur in the EXT1 and EXT2 genes in Chinese kindreds with multiple osteochondromas. (PMID:23629877)
  • This study demonstrated no association of rs1113132, rs3740878 and rs11037909 EXT2 variants with type 2 diabetes mellitus. (PMID:23871501)
  • these findings are useful for extending the mutational spectrum in EXT1 and EXT2 and understanding the genetic basis of multiple osteochondromas in Chinese patients. (PMID:24120389)
  • EXT1 and EXT2 heterozygous mutations in 18 (54.6 %) and ten (30.3 %) probands respectively, which represents a total of 28 (84.9 %) index cases. (PMID:24532482)
  • The heterozygous mutation c.743+1G>A in the EXT2 gene causes HME as a result of abnormal splicing, mRNA decay, and the resulting haploinsufficiency of EXT2. (PMID:24728384)
  • EXT2 gene might not have a major role in the development of type 2 diabetes in the Chinese population. (PMID:25207843)
  • EXT2 mutation is associated with multiple osteochondromatosis. (PMID:25230886)
  • The second exon of EXT2. A c.244delG mutation is associated with hereditary multiple exostosis. (PMID:25449079)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioext2ENSDARG00000056648
mus_musculusExt2ENSMUSG00000027198
rattus_norvegicusExt2ENSRNOG00000008944
drosophila_melanogastersotvFBGN0029175

Paralogs (4): EXTL3 (ENSG00000012232), EXTL1 (ENSG00000158008), EXTL2 (ENSG00000162694), EXT1 (ENSG00000182197)

Protein

Protein identifiers

Exostosin-2Q93063 (reviewed: Q93063)

Alternative names: Exostosin glycosyltransferase 2, Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase, Heparan sulfate co-polymerase subunit EXT1, Multiple exostoses protein 2

All UniProt accessions (8): A0A804HHX4, A0A804HIU8, A0A804HJW9, A0A804HKG2, A0A804HKG8, A0A804HL74, A0A804HLF7, Q93063

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase forming with EXT1 the heterodimeric heparan sulfate polymerase which catalyzes the elongation of the heparan sulfate glycan backbone. Glycan backbone extension consists in the alternating transfer of (1->4)-beta-D-GlcA and (1->4)-alpha-D-GlcNAc residues from their respective UDP-sugar donors. Both EXT1 and EXT2 are required for the full activity of the polymerase since EXT1 bears the N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity within the complex while EXT2 carries the glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity. Heparan sulfate proteoglycans are ubiquitous components of the extracellular matrix and play an important role in tissue homeostasis and signaling.

Subunit / interactions. Part of the heparan sulfate polymerase, a dimeric complex composed of EXT1 and EXT2. Could also form homooligomeric complexes. Interacts with NDST1. Interacts with GALNT5.

Subcellular location. Golgi apparatus membrane. Golgi apparatus. cis-Golgi network membrane. Endoplasmic reticulum membrane. Secreted.

Tissue specificity. Widely expressed.

Post-translational modifications. N-glycosylated at Asn-637. A soluble form is generated by proteolytic processing.

Disease relevance. Hereditary multiple exostoses 2 (EXT2) [MIM:133701] EXT is a genetically heterogeneous bone disorder caused by genes segregating on human chromosomes 8, 11, and 19 and designated EXT1, EXT2 and EXT3 respectively. EXT is a dominantly inherited skeletal disorder primarily affecting endochondral bone during growth. The disease is characterized by formation of numerous cartilage-capped, benign bone tumors (osteocartilaginous exostoses or osteochondromas) that are often accompanied by skeletal deformities and short stature. In a small percentage of cases exostoses have exhibited malignant transformation resulting in an osteosarcoma or chondrosarcoma. Osteochondromas development can also occur as a sporadic event. The disease is caused by variants affecting the gene represented in this entry. Seizures, scoliosis, and macrocephaly/microcephaly syndrome (SSMS) [MIM:616682] An autosomal recessive syndrome characterized by seizures, intellectual disability, hypotonia, scoliosis, macrocephaly, hypertelorism and renal dysfunction. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 47 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q93063-11yes
Q93063-22
Q93063-33

RefSeq proteins (5): NP_000392, NP_001171554, NP_001376557, NP_001376559, NP_997005* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004263ExostosinFamily
IPR015338GT64_domDomain
IPR029044Nucleotide-diphossugar_transHomologous_superfamily
IPR040911Exostosin_GT47Domain

Pfam: PF03016, PF09258

Enzyme classification (BRENDA):

  • EC 2.4.1.224 — glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase (BRENDA: 10 organisms, 19 substrates, 0 inhibitors, 8 Km, 0 kcat entries)
  • EC 2.4.1.225 — N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase (BRENDA: 9 organisms, 7 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
UDP-N-ACETYL-D-GLUCOSAMINE0.094–1.24
(MANNOSE)9-N-ACETYL-D-GLUCOSAMINE0.651
[D-GLUCURONIC ACID-N-ACETYL-GLUCOSAMINE]14 -D-GL0.0061
[D-GLUCURONIC ACID-N-ACETYL-GLUCOSAMINE]4 -D-GLU0.061

Catalyzed reactions (Rhea), 1 shown:

UniProt features (120 total): strand 28, helix 25, binding site 21, sequence variant 11, mutagenesis site 10, turn 9, disulfide bond 5, sequence conflict 3, topological domain 2, glycosylation site 2, splice variant 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
7SCKELECTRON MICROSCOPY2.8
7ZAYELECTRON MICROSCOPY2.8
7UQYELECTRON MICROSCOPY3
7SCHELECTRON MICROSCOPY3.1
7UQXELECTRON MICROSCOPY3.3
7SCJELECTRON MICROSCOPY3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q93063-F187.590.67

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (21): 517; 522; 538; 538; 539; 539; 540; 540; 582; 584; 627; 628

Disulfide bonds (5): 85–90, 96–151, 286–300, 318–339, 626–676

Glycosylation sites (2): 288, 637

Mutagenesis-validated functional residues (10):

PositionPhenotype
266no effect on n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity.
308increased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. decreased glucuronosyl-n-acetylgluc
325increased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. no effect on glucuronosyl-n-acetylg
328no effect on n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. no effect on glucuronosyl-n-acet
538decreased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. loss of glucuronosyl-n-acetylglucos
538decreased glucuronosyl-n-acetylglucosaminyl-proteoglycan 4-alpha-n-acetylglucosaminyltransferase activity; when associat
540increased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. decreased glucuronosyl-n-acetylgluc
540decreased glucuronosyl-n-acetylglucosaminyl-proteoglycan 4-alpha-n-acetylglucosaminyltransferase activity; when associat
569increased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. loss of glucuronosyl-n-acetylglucos
585decreased n-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity. decreased glucuronosyl-n-acetylgluc

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-2022928HS-GAG biosynthesis
R-HSA-3656237Defective EXT2 causes exostoses 2
R-HSA-3656253Defective EXT1 causes exostoses 1, TRPS2 and CHDS

MSigDB gene sets: 453 (showing top): GOBP_POLYSACCHARIDE_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_BLOOD_PRESSURE, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_FORMATION_OF_PRIMARY_GERM_LAYER, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, GOBP_SULFATION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, CCANNAGRKGGC_UNKNOWN

GO Biological Process (19): polysaccharide biosynthetic process (GO:0000271), ossification (GO:0001503), mesoderm formation (GO:0001707), chondrocyte differentiation (GO:0002062), glycosaminoglycan biosynthetic process (GO:0006024), protein N-linked glycosylation (GO:0006487), regulation of blood pressure (GO:0008217), gene expression (GO:0010467), heparan sulfate proteoglycan biosynthetic process (GO:0015012), heparin proteoglycan biosynthetic process (GO:0030210), fluid transport (GO:0042044), vasodilation (GO:0042311), cellular response to fibroblast growth factor stimulus (GO:0044344), multicellular organismal-level water homeostasis (GO:0050891), sulfation (GO:0051923), sodium ion homeostasis (GO:0055078), heart contraction (GO:0060047), endochondral bone morphogenesis (GO:0060350), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (10): glucuronosyltransferase activity (GO:0015020), glycosyltransferase activity (GO:0016757), heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328), metal ion binding (GO:0046872), protein heterodimerization activity (GO:0046982), glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508), N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509), protein binding (GO:0005515), acetylglucosaminyltransferase activity (GO:0008375), transferase activity (GO:0016740)

GO Cellular Component (9): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), membrane (GO:0016020), UDP-N-acetylglucosamine transferase complex (GO:0043541), extracellular exosome (GO:0070062), catalytic complex (GO:1902494), extracellular region (GO:0005576), endoplasmic reticulum membrane (GO:0005789)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Diseases associated with glycosaminoglycan metabolism2
Heparan sulfate/heparin (HS-GAG) metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
macromolecule biosynthetic process2
blood circulation2
protein O-linked glycosylation via xylose2
UDP-glycosyltransferase activity2
hexosyltransferase activity2
acetylglucosaminyltransferase activity2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
cellular anatomical structure2
polysaccharide metabolic process1
carbohydrate biosynthetic process1
multicellular organismal process1
formation of primary germ layer1
mesoderm morphogenesis1
cell differentiation1
cartilage development1
aminoglycan biosynthetic process1
glycosaminoglycan metabolic process1
glycoprotein biosynthetic process1
regulation of biological quality1
proteoglycan biosynthetic process1
heparan sulfate proteoglycan metabolic process1
heparin proteoglycan metabolic process1
transport1
blood vessel diameter maintenance1
cellular response to growth factor stimulus1
response to fibroblast growth factor1
regulation of body fluid levels1
multicellular organismal-level chemical homeostasis1
sulfur compound metabolic process1
monoatomic cation homeostasis1
inorganic ion homeostasis1
heart process1
bone morphogenesis1
transferase activity1
cation binding1
protein dimerization activity1
glucuronosyltransferase activity1
binding1

Protein interactions and networks

STRING

1044 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EXT2EXT1Q16394986
EXT2NDST1P52848941
EXT2ALX4Q9H161912
EXT2HHEXQ03014784
EXT2HS2ST1Q7LGA3774
EXT2SLC30A8Q8IWU4768
EXT2POLR1FQ3B726748
EXT2NDST2P52849742
EXT2DUSP16Q9BY84677
EXT2SLC35B2Q8TB61670
EXT2B4GALT7Q9UBV7668
EXT2TRAP1Q12931663
EXT2K7EP71K7EP71663
EXT2KIF11P52732658
EXT2B3GAT3O94766657

IntAct

88 interactions, top by confidence:

ABTypeScore
PIK3CAPIK3R2psi-mi:“MI:0914”(association)0.900
EXT1EXT2psi-mi:“MI:2364”(proximity)0.890
EXT1EXT2psi-mi:“MI:0407”(direct interaction)0.890
SLC39A5FAM171A2psi-mi:“MI:0914”(association)0.640
EXT2SLC22A2psi-mi:“MI:0915”(physical association)0.550
GSKIPEXT2psi-mi:“MI:0915”(physical association)0.370
EXT2ANXA7psi-mi:“MI:0915”(physical association)0.370
CDKN1AEXT2psi-mi:“MI:0915”(physical association)0.370
PFDN1EXT2psi-mi:“MI:0915”(physical association)0.370
EXT2SMN1psi-mi:“MI:0915”(physical association)0.370
TK1EXT2psi-mi:“MI:0915”(physical association)0.370
M2IPO5psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
TMEM106AQSOX1psi-mi:“MI:0914”(association)0.350
MPPE1FAM234Bpsi-mi:“MI:0914”(association)0.350
PSCAMETTL15psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
GPIHBP1SAC3D1psi-mi:“MI:0914”(association)0.350
TMPRSS13TOR1Apsi-mi:“MI:0914”(association)0.350
HPNTOR1Apsi-mi:“MI:0914”(association)0.350
EXT2EXTL3psi-mi:“MI:0914”(association)0.350
TMEM106ATMEM131Lpsi-mi:“MI:0914”(association)0.350
HLA-CTMEM131Lpsi-mi:“MI:0914”(association)0.350

BioGRID (110): EXT2 (Affinity Capture-MS), INVS (Affinity Capture-MS), TTC19 (Affinity Capture-MS), RBFA (Affinity Capture-MS), EXT1 (Affinity Capture-MS), AFAP1 (Affinity Capture-MS), ATE1 (Affinity Capture-MS), CUX1 (Affinity Capture-MS), USP30 (Affinity Capture-MS), NOP9 (Affinity Capture-MS), HLA-DPB1 (Affinity Capture-MS), STK16 (Affinity Capture-MS), SNCG (Affinity Capture-MS), HYOU1 (Affinity Capture-MS), CNTF (Affinity Capture-MS)

ESM2 similar proteins: A4IID1, A5D7I4, A5PK45, A9X1C8, G5E897, O12971, O60568, O77783, O95803, P52848, P52849, P52850, P70428, P97464, Q02353, Q16394, Q3UHN9, Q5F407, Q5IGR6, Q5IGR7, Q5IGR8, Q5M854, Q5R6K5, Q5RBC3, Q5U367, Q5U4X8, Q6EV56, Q6GMK0, Q6GQI7, Q6GQK9, Q6IS24, Q6UW63, Q6ZQ11, Q7TT15, Q7Z4H8, Q812F8, Q86X52, Q8K297, Q8NBJ5, Q8VHI3

Diamond homologs: A2Y6Z7, O01705, O43909, O77783, P70428, Q53WK1, Q5IGR8, Q5RBC3, Q84WB7, Q93063, Q9WVL6, Q9XZ08, Q9Y169, A5D7I4, A9X1C8, O01704, P97464, Q16394, Q33AH8, Q5IGR6, Q5IGR7, Q92935, Q9C975, Q9ES89, Q9JK82, Q9JKV7, Q9LY62, Q9SSE8, Q9UBQ6, Q9V730, A9RGD8, Q10SX7, Q3E9A4, Q3EAR7, Q6H4N0, Q6NMM8, Q7XLG3, Q8S1X7, Q8S1X8, Q8S1X9

SIGNOR signaling

1 interactions.

AEffectBMechanism
EXT2“form complex”EXT1/EXT2binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

1033 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic196
Likely pathogenic41
Uncertain significance404
Likely benign247
Benign55

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1069929NM_207122.2(EXT2):c.282T>A (p.Tyr94Ter)Pathogenic
1073638NM_207122.2(EXT2):c.1234C>T (p.Gln412Ter)Pathogenic
1073639NM_207122.2(EXT2):c.1287G>A (p.Trp429Ter)Pathogenic
1074447NM_207122.2(EXT2):c.64_68del (p.His22fs)Pathogenic
1076808NM_207122.2(EXT2):c.1577dup (p.Tyr526Ter)Pathogenic
1076816NM_207122.2(EXT2):c.783_784del (p.His262fs)Pathogenic
1175790NM_207122.2(EXT2):c.484C>T (p.Gln162Ter)Pathogenic
1211965NM_207122.2(EXT2):c.536+1G>APathogenic
1224433NM_207122.2(EXT2):c.540G>A (p.Trp180Ter)Pathogenic
1251963NM_207122.2(EXT2):c.728del (p.Pro243fs)Pathogenic
1351327NM_207122.2(EXT2):c.516del (p.Ala173fs)Pathogenic
1352684NM_207122.2(EXT2):c.680A>G (p.Asp227Gly)Pathogenic
1376872NM_207122.2(EXT2):c.1080-2A>GPathogenic
1378644NM_207122.2(EXT2):c.1080-1G>APathogenic
1382216NM_207122.2(EXT2):c.729del (p.Glu244fs)Pathogenic
1386232NM_207122.2(EXT2):c.398_402del (p.Leu133fs)Pathogenic
1392678NM_207122.2(EXT2):c.537-4_561delPathogenic
1405824NM_207122.2(EXT2):c.620_626+158delPathogenic
1407563NM_207122.2(EXT2):c.705_706del (p.Leu236fs)Pathogenic
1409142NM_207122.2(EXT2):c.779del (p.Gly260fs)Pathogenic
1414023NM_207122.2(EXT2):c.1824T>A (p.Tyr608Ter)Pathogenic
1417949NM_207122.2(EXT2):c.1013del (p.Gly338fs)Pathogenic
1427412NM_207122.2(EXT2):c.750del (p.Gln251fs)Pathogenic
1432441NM_207122.2(EXT2):c.1003_1004insA (p.Leu335fs)Pathogenic
1451350NM_207122.2(EXT2):c.939+1delPathogenic
1454141NM_207122.2(EXT2):c.89del (p.Phe30fs)Pathogenic
1455305NM_207122.2(EXT2):c.1201del (p.Gln401fs)Pathogenic
1456520NM_207122.2(EXT2):c.1080-1G>TPathogenic
1456787NM_207122.2(EXT2):c.1080-2delPathogenic
1457792NM_207122.2(EXT2):c.244dup (p.Asp82fs)Pathogenic

SpliceAI

2264 predictions. Top by Δscore:

VariantEffectΔscore
11:44104768:G:GTdonor_gain1.0000
11:44107673:T:Aacceptor_gain1.0000
11:44114179:TTTCA:Tacceptor_loss1.0000
11:44114180:TTCA:Tacceptor_loss1.0000
11:44114181:TCA:Tacceptor_loss1.0000
11:44114182:CAGG:Cacceptor_loss1.0000
11:44114183:A:Cacceptor_loss1.0000
11:44114184:G:GTacceptor_loss1.0000
11:44114300:GG:Gdonor_gain1.0000
11:44114301:GG:Gdonor_gain1.0000
11:44124787:A:AGacceptor_gain1.0000
11:44124788:G:GGacceptor_gain1.0000
11:44126811:TGCAG:Tacceptor_loss1.0000
11:44126812:GCAGG:Gacceptor_loss1.0000
11:44126813:CA:Cacceptor_loss1.0000
11:44126813:CAGG:Cacceptor_gain1.0000
11:44126814:AG:Aacceptor_gain1.0000
11:44126814:AGGA:Aacceptor_gain1.0000
11:44126814:AGGAG:Aacceptor_gain1.0000
11:44126815:GG:Gacceptor_gain1.0000
11:44126815:GGAG:Gacceptor_gain1.0000
11:44126815:GGAGG:Gacceptor_gain1.0000
11:44126951:AAGAG:Adonor_loss1.0000
11:44126952:AGAGG:Adonor_loss1.0000
11:44126953:GAG:Gdonor_gain1.0000
11:44126953:GAGG:Gdonor_loss1.0000
11:44126954:AGG:Adonor_loss1.0000
11:44126957:T:Gdonor_loss1.0000
11:44126961:T:TAdonor_gain1.0000
11:44126962:A:AAdonor_gain1.0000

AlphaMissense

4723 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:44107998:T:AC96S1.000
11:44107999:G:CC96S1.000
11:44108163:T:CC151R1.000
11:44108164:G:AC151Y1.000
11:44108165:T:GC151W1.000
11:44171687:G:CR417P1.000
11:44197890:T:CF456S1.000
11:44197896:C:AA458D1.000
11:44197905:T:CL461P1.000
11:44197917:G:CR465P1.000
11:44197983:T:AV487D1.000
11:44197986:T:AV488D1.000
11:44197988:T:AW489R1.000
11:44197988:T:CW489R1.000
11:44197990:G:CW489C1.000
11:44197990:G:TW489C1.000
11:44197993:T:AN490K1.000
11:44197993:T:GN490K1.000
11:44206853:T:CL519S1.000
11:44206855:A:CS520R1.000
11:44206857:T:AS520R1.000
11:44206857:T:GS520R1.000
11:44206861:C:AR522S1.000
11:44206864:T:CF523L1.000
11:44206865:T:CF523S1.000
11:44206866:C:AF523L1.000
11:44206866:C:GF523L1.000
11:44206901:T:CL535P1.000
11:44206909:G:CD538H1.000
11:44206910:A:CD538A1.000

dbSNP variants (sampled 300 via entrez): RS1000002649 (11:44146601 T>C), RS1000009999 (11:44192850 G>C), RS1000023977 (11:44160639 A>G), RS1000035219 (11:44146903 T>A), RS1000038363 (11:44238900 A>G,T), RS1000040374 (11:44106264 G>C), RS1000051872 (11:44101584 C>A,G,T), RS1000096303 (11:44179535 G>A), RS1000103115 (11:44139899 G>A), RS1000118498 (11:44160295 T>C), RS1000126742 (11:44251951 G>A,C), RS1000146507 (11:44113198 G>T), RS1000153488 (11:44126064 T>C), RS1000170676 (11:44226430 G>A), RS1000190878 (11:44219825 C>G)

Disease associations

OMIM: gene MIM:608210 | disease phenotypes: MIM:133701, MIM:133700, MIM:616682, MIM:167000

GenCC curated gene-disease

DiseaseClassificationInheritance
exostoses, multiple, type 2DefinitiveAutosomal dominant
seizures-scoliosis-macrocephaly syndromeStrongAutosomal recessive
hereditary multiple osteochondromasSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
exostoses, multiple, type 2DefinitiveAD

Mondo (7): exostoses, multiple, type 2 (MONDO:0007586), hereditary multiple osteochondromas (MONDO:0005508), seizures-scoliosis-macrocephaly syndrome (MONDO:0014731), exostoses, multiple, type 1 (MONDO:0007585), hepatoblastoma (MONDO:0018666), ovarian cancer (MONDO:0008170), hereditary neoplastic syndrome (MONDO:0015356)

Orphanet (5): Multiple osteochondromas (Orphanet:321), Seizures-scoliosis-macrocephaly syndrome (Orphanet:466926), Hepatoblastoma (Orphanet:449), Rare ovarian cancer (Orphanet:213500), Inherited cancer-predisposing syndrome (Orphanet:140162)

HPO phenotypes

142 total (30 of 142 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000016Urinary retention
HP:0000028Cryptorchidism
HP:0000054Micropenis
HP:0000077Abnormality of the kidney
HP:0000093Proteinuria
HP:0000248Brachycephaly
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000322Short philtrum
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000356Abnormality of the outer ear
HP:0000384Preauricular skin tag
HP:0000414Bulbous nose
HP:0000426Prominent nasal bridge
HP:0000430Underdeveloped nasal alae
HP:0000437Depressed nasal tip
HP:0000455Broad nasal tip
HP:0000486Strabismus
HP:0000639Nystagmus
HP:0000717Autism
HP:0000729Autistic behavior
HP:0000733Motor stereotypy
HP:0000750Delayed speech and language development

GWAS associations

3 associations (top):

StudyTraitp-value
GCST008163_130Height8.000000e-06
GCST010002_236Refractive error2.000000e-24
GCST010396_281Gut microbiota (bacterial taxa, hurdle binary method)7.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007874gut microbiome measurement

MeSH disease descriptors (4)

DescriptorNameTree numbers
D005097Exostoses, Multiple HereditaryC04.557.450.565.575.610.615.325; C04.700.330; C05.116.099.708.670.615.325; C05.116.540.310.500; C16.320.700.330
D018197HepatoblastomaC04.557.435.380
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
D010051Ovarian NeoplasmsC04.588.322.455; C12.050.351.500.056.630.705; C12.050.351.937.418.685; C12.100.250.056.630.705; C12.900.418.685; C19.344.410; C19.391.630.705

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression5
sodium arseniteincreases expression, decreases expression, affects cotreatment, increases abundance3
Air Pollutantsdecreases expression, increases abundance2
bisphenol Fincreases expression, affects cotreatment1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
mono-(2-ethylhexyl)phthalatedecreases methylation, increases abundance1
perfluorooctanoic aciddecreases expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ICG 001increases expression1
Acetaminophenincreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Carbamazepineaffects expression1
Cisplatinincreases expression1
Cycloheximidedecreases expression, decreases reaction1
Cytarabinedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylhexyl Phthalatedecreases methylation, increases abundance1
Doxorubicindecreases expression1
Estradiolaffects expression1
Indomethacinaffects cotreatment, increases expression1
Seleniumdecreases expression1
Smokedecreases expression, increases abundance1
Tetrachlorodibenzodioxindecreases reaction, decreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Aflatoxin B1decreases methylation1
Sodium Seleniteincreases expression1
Copper Sulfatedecreases expression1

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C768ESe026-AEmbryonic stem cellMale
CVCL_SM62HAP1 EXT2 (-) 1Cancer cell lineMale
CVCL_SM63HAP1 EXT2 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT02933333PHASE4UNKNOWNG-CSF Alone or Combination With GM-CSF on Prevention and Treatment of Infection in Children With Malignant Tumor
NCT00190697PHASE4COMPLETEDA Study of LY353381 (Arzoxifene) for Patients Who Benefitted From This Drug in Other Oncology Trials and Wished to Continue Treatment
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00727961PHASE4COMPLETEDA Study to Evaluate Efficacy and Tolerance of Caelyx in Patients With Epithelial Ovarian Cancer. (Study P04072)(COMPLETED)
NCT00740116PHASE4COMPLETEDTranexamic Acid in Surgery of Advanced Ovarian Cancer
NCT00817479PHASE4COMPLETEDTumor Gene Expression in Women With Ovarian Cancer
NCT01432015PHASE4COMPLETEDFosaprepitant Versus Aprepitant in the Prevention of Chemotherapy Induced Nausea and Vomiting
NCT01706120PHASE4UNKNOWNStudy of Clinical and Biological Prognostic Factors in Patients With Ovarian Cancer Receiving Carboplatin +Paclitaxel With Bevacizumab
NCT01932125PHASE4COMPLETEDAn Interventional Study of Avastin (Bevacizumab) in Patients With Advanced/Metastatic Epithelial Ovarian Cancer, Fallopian Tube Cancer or Primary Peritoneal Cancer
NCT01953107PHASE4COMPLETEDOral Iron vs. Placebo in Newly Diagnosed Gynecologic Oncology Patients Who Are Surgical Candidates.
NCT02035345PHASE4TERMINATEDSlowed Carboplatin Infusion for Ovarian Cancer Patients Receiving Carboplatin Re-Treatment
NCT02243059PHASE4WITHDRAWNMagnetic Resonance Imaging for Lymph Node Staging in Ovarian Cancer
NCT03164980PHASE4TERMINATEDQoL-Comparison Between Trabectedin/PLD and Pt-based Therapy in Patients With Pt-sensitive Recurrent Ovarian Cancer
NCT03384511PHASE4COMPLETEDThe Use of 18F-ALF-NOTA-PRGD2 PET/CT Scan to Predict the Efficacy and Adverse Events of Apatinib in Malignancies.
NCT03543462PHASE4COMPLETEDDiaphragmatic Resection And Gynecological Ovarian Neoplasm
NCT03752216PHASE4COMPLETEDNIraparib and Quality of LifE is a Longitudinal Study Evaluating in Real Life the Tolerability of Niraparib.
NCT03858166PHASE4TERMINATEDEfficacy and Safety of PEG-rhG-CSF Secondary Prophylaxis vs. Therapeutic Administration in Patients With Ovarian Cancer
NCT04024254PHASE4COMPLETEDA Study of Serum Folate Levels in Patients Treated With Olaparib
NCT04330040PHASE4COMPLETEDProspective Multicentre Phase-IV Clinical Trial of Olaparib in Indian Patients With Ovarian and Metastatic Breast Cancer
NCT04352439PHASE4COMPLETEDAspirin for Prevention of Venous Thromboembolism Among Ovarian Cancer Patients Receiving Neoadjuvant Chemotherapy
NCT05187208PHASE4UNKNOWNPARP Inhibitor Oral Maintenance in Low-Risk Ovarian Cancer
NCT05606692PHASE4RECRUITINGInfluences of Propofol and Sevoflurane Anesthesia in Ovarian Cancer (Anesthetics)
NCT05926336PHASE4RECRUITINGThe Effects of Using Different Anesthetics on the Prognosis of Primary Tumors and Its Mechanism of Action
NCT06412120PHASE4RECRUITINGStudy Evaluating Safety, Tolerability, and Metabolism of Niraparib
NCT06871787PHASE4NOT_YET_RECRUITINGNear-Infrared Fluorescence Imaging With Indocyanine Green to Evaluate Bowel Anastomoses in Gynecologic Oncology Surgery
NCT06887933PHASE4NOT_YET_RECRUITINGA Trial to Evaluate the Safety of Niraparib Tablets in Adult Female Participants With Advanced or Relapsed Epithelial Ovarian Cancer
NCT07469202PHASE4NOT_YET_RECRUITINGCYTALUX Dose Extension Study
NCT03017326PHASE3ACTIVE_NOT_RECRUITINGPaediatric Hepatic International Tumour Trial
NCT03533582PHASE3ACTIVE_NOT_RECRUITINGCisplatin and Combination Chemotherapy in Treating Children and Young Adults With Hepatoblastoma or Liver Cancer After Surgery
NCT04478292PHASE3RECRUITINGA Multi-institutional Study for Treatment of Children With Newly Diagnosed Hepatoblastoma Using a Modified PHITT Strategy
NCT00001806PHASE3COMPLETEDMethods in Education for Breast Cancer Genetics
NCT00002477PHASE3UNKNOWNAdjuvant Chemotherapy Compared With Observation in Treating Patients With Resected Early Stage Ovarian Epithelial Cancer
NCT00002568PHASE3COMPLETEDCombination Chemotherapy With or Without Surgery in Treating Patients With Stage III Ovarian Epithelial Cancer
NCT00002641PHASE3COMPLETEDSurgery With or Without Chemotherapy in Treating Patients With Soft Tissue Sarcoma
NCT00002717PHASE3COMPLETEDPaclitaxel and Cisplatin in Treating Patients With Stage III or Stage IV Ovarian Cancer or Primary Peritoneal Cancer
NCT00002764PHASE3COMPLETEDSurgery With or Without Combination Chemotherapy in Treating Patients With Lung Metastases From Soft Tissue Sarcoma
NCT00002819PHASE3TERMINATEDChemotherapy With or Without Peripheral Stem Cell Transplantation in Treating Patients With Persistent Ovarian Epithelial Cancer
NCT00002894PHASE3COMPLETEDPlatinum-based Chemotherapy With or Without Paclitaxel in Treating Patients With Relapsed Ovarian Cancer
NCT00002895PHASE3COMPLETEDEarly Chemotherapy Based on CA 125 Level Alone Compared With Delayed Chemotherapy in Treating Patients With Recurrent Ovarian Epithelial , Fallopian Tube, or Primary Peritoneal Cancer
NCT00003120PHASE3COMPLETEDS9701 Paclitaxel in Treating Patients With Advanced Ovarian, Fallopian Tube, or Primary Peritoneal Cancer in Remission