ESS2

gene
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Also known as DGSIEs2elES2DGS-HESS-2bis1

Summary

ESS2 (ess-2 spliceosome associated protein, HGNC:16817) is a protein-coding gene on chromosome 22q11.21, encoding Splicing factor ESS-2 homolog (Q96DF8). May be involved in pre-mRNA splicing. It is a common-essential gene (DepMap: required in 97.0% of cancer cell lines).

This gene is located within the minimal DGS critical region (MDGCR) thought to contain the gene(s) responsible for a group of developmental disorders. These disorders include DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome, and some familial or sporadic conotruncal cardiac defects which have been associated with microdeletion of 22q11.2. The encoded protein may be a component of C complex spliceosomes, and the orthologous protein in the mouse localizes to the nucleus. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 8220 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 205 total — 1 pathogenic
  • Phenotypes (HPO): 39
  • Cancer dependency (DepMap): dependent in 97.0% of screened cell lines (common-essential)
  • MANE Select transcript: NM_022719

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16817
Approved symbolESS2
Nameess-2 spliceosome associated protein
Location22q11.21
Locus typegene with protein product
StatusApproved
AliasesDGSI, Es2el, ES2, DGS-H, ESS-2, bis1
Ensembl geneENSG00000100056
Ensembl biotypeprotein_coding
OMIM601755
Entrez8220

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000252137, ENST00000434568, ENST00000469466, ENST00000472073, ENST00000909110, ENST00000909111, ENST00000909112, ENST00000951415, ENST00000951416

RefSeq mRNA: 1 — MANE Select: NM_022719 NM_022719

CCDS: CCDS13756

Canonical transcript exons

ENST00000252137 — 10 exons

ExonStartEnd
ENSE000008790931913027919134475
ENSE000034705601913506019135175
ENSE000035096461913985519140024
ENSE000035243041913821519138317
ENSE000035364501913732319137432
ENSE000035683801914272619142894
ENSE000036124191913961219139729
ENSE000036330461914253819142633
ENSE000036352501913915919139292
ENSE000038481101914450619144651

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 88.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1665 / max 124.5055, expressed in 1814 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
19313115.90981814
1931320.2566125

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001988.96gold quality
right testisUBERON:000453488.56gold quality
left testisUBERON:000453388.47gold quality
granulocyteCL:000009487.20gold quality
testisUBERON:000047386.76gold quality
male germ cellCL:000001586.65gold quality
bloodUBERON:000017885.28gold quality
skin of legUBERON:000151184.47gold quality
skin of abdomenUBERON:000141683.91gold quality
lower esophagus muscularis layerUBERON:003583383.85gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.84gold quality
lower esophagusUBERON:001347383.83gold quality
popliteal arteryUBERON:000225083.66gold quality
tibial arteryUBERON:000761083.66gold quality
sural nerveUBERON:001548883.57gold quality
esophagogastric junction muscularis propriaUBERON:003584183.53gold quality
cortical plateUBERON:000534383.52gold quality
adult organismUBERON:000702383.45gold quality
oocyteCL:000002383.43gold quality
aortaUBERON:000094783.15gold quality
prefrontal cortexUBERON:000045182.92gold quality
mucosa of stomachUBERON:000119982.87gold quality
zone of skinUBERON:000001482.76gold quality
left uterine tubeUBERON:000130382.74gold quality
thoracic aortaUBERON:000151582.74gold quality
descending thoracic aortaUBERON:000234582.70gold quality
muscle layer of sigmoid colonUBERON:003580582.68gold quality
apex of heartUBERON:000209882.67gold quality
body of uterusUBERON:000985382.66gold quality
ascending aortaUBERON:000149682.59gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

117 targeting ESS2, 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-4481100.0066.421669
HSA-MIR-4455100.0065.481587
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-302E99.9670.742669
HSA-MIR-545-3P99.9570.742783
HSA-MIR-22-3P99.9368.13917
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
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-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-444799.8567.812900
HSA-MIR-373-3P99.8470.681668
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-187-5P99.7470.261404
HSA-MIR-4446-5P99.7269.192544
HSA-MIR-453099.6966.471509
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-452-5P99.6569.631762

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

  • Experiments using Ess2 deletion mutants showed that a C-terminus deletion mutant of Ess2 (1-399 a. a.) lost its ability to associate with snRNAs, whereas the N-terminus domain of Ess2 (1-200 a. a.) associated with retinoic acid receptor-related orphan receptor gamma/gamma-t, but not with snRNAs. (PMID:29454968)
  • Transcriptional coregulator Ess2 controls survival of post-thymic CD4(+) T cells through the Myc and IL-7 signaling pathways. (PMID:35933014)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioess2ENSDARG00000060922
mus_musculusEss2ENSMUSG00000003527
rattus_norvegicusEss2ENSRNOG00000000283
drosophila_melanogasterEs2FBGN0023506
caenorhabditis_elegansWBGENE00018371

Protein

Protein identifiers

Splicing factor ESS-2 homologQ96DF8 (reviewed: Q96DF8)

Alternative names: DiGeorge syndrome critical region 13, DiGeorge syndrome critical region 14, DiGeorge syndrome protein H, Protein ES2

All UniProt accessions (2): Q96DF8, F8WEF8

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in pre-mRNA splicing.

Subunit / interactions. Identified in the spliceosome C complex. Interacts with FRA10AC1.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in heart, brain and skeletal muscle. Detected at low levels in placenta.

Similarity. Belongs to the ESS2 family.

RefSeq proteins (1): NP_073210* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019148Nuclear_protein_DGCR14_ESS-2Family

Pfam: PF09751

UniProt features (18 total): modified residue 6, compositionally biased region 4, region of interest 3, sequence variant 3, chain 1, cross-link 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
8C6JELECTRON MICROSCOPY2.8
9FMDELECTRON MICROSCOPY3.3
8RO2ELECTRON MICROSCOPY3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DF8-F168.410.13

Functional residue map

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

Post-translational modifications (7): 292, 386, 391, 395, 142, 1, 3

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 176 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, MODULE_70, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_RNA_SPLICING, LIAO_METASTASIS, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, KIM_WT1_TARGETS_DN, STARK_HYPPOCAMPUS_22Q11_DELETION_DN, MARTENS_TRETINOIN_RESPONSE_UP

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), nervous system development (GO:0007399), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), catalytic step 2 spliceosome (GO:0071013), spliceosomal complex (GO:0005681)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
system development1
mRNA metabolic process1
binding1
intracellular membrane-bounded organelle1
Prp19 complex1
spliceosomal complex1
U5 snRNP1
catalytic complex1
nuclear protein-containing complex1
ribonucleoprotein complex1

Protein interactions and networks

STRING

970 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESS2GATD3P0DPI2925
ESS2DGCR2P98153856
ESS2SOX2P48431838
ESS2SLC25A1P53007809
ESS2ESR1P03372801
ESS2HIRAP54198726
ESS2SUZ12Q15022725
ESS2UFD1Q92890710
ESS2CLTCL1P53675704
ESS2RPS7P23821609
ESS2EPCAMP16422559
ESS2HNRNPA1P09651548
ESS2CLTCQ00610548
ESS2HNRNPH2P55795511
ESS2HNRNPH1P31943495

IntAct

160 interactions, top by confidence:

ABTypeScore
PPIEAQRpsi-mi:“MI:0914”(association)0.810
ISY1AQRpsi-mi:“MI:0914”(association)0.740
FRA10AC1ESS2psi-mi:“MI:0915”(physical association)0.730
SNRPGGEMIN2psi-mi:“MI:0914”(association)0.710
SNW1AQRpsi-mi:“MI:0914”(association)0.650
SNRPA1HTATSF1psi-mi:“MI:0914”(association)0.640
SNRPA1U2SURPpsi-mi:“MI:0914”(association)0.640
ESS2ACADSpsi-mi:“MI:0914”(association)0.640
ESS2PRPF19psi-mi:“MI:0915”(physical association)0.620
ARMC7ESS2psi-mi:“MI:0915”(physical association)0.560
CCDC57ESS2psi-mi:“MI:0915”(physical association)0.560
DGCR6ESS2psi-mi:“MI:0915”(physical association)0.560
OIP5ESS2psi-mi:“MI:0915”(physical association)0.560
ESS2SMARCD1psi-mi:“MI:0915”(physical association)0.560
ESS2NXF1psi-mi:“MI:0915”(physical association)0.560
EXOC8ESS2psi-mi:“MI:0915”(physical association)0.560
ESS2ARMC7psi-mi:“MI:0915”(physical association)0.560
QARS1ESS2psi-mi:“MI:0915”(physical association)0.560
ESS2GFAPpsi-mi:“MI:0915”(physical association)0.560
ESS2JPH3psi-mi:“MI:0915”(physical association)0.560

BioGRID (199): DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Synthetic Lethality), DGCR14 (Proximity Label-MS), DGCR14 (Proximity Label-MS), DGCR14 (Proximity Label-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS), DGCR14 (Affinity Capture-MS)

ESM2 similar proteins: A1A4P4, A1CH36, A2ALW5, A5AAL8, B0BN56, O42911, O70279, P0C2B7, P58468, P83565, Q0CLE8, Q1ECT8, Q290P4, Q2GVC2, Q3SZ86, Q4G0I0, Q4V7Q1, Q5B4U6, Q5BJW9, Q5RFR4, Q5XJW2, Q61733, Q6RUT7, Q753F1, Q7SDU5, Q7SHR9, Q80ZS3, Q86TS9, Q8BGX2, Q8BK72, Q8CHP5, Q8SPE7, Q8TAE8, Q8VD26, Q8WUQ7, Q96AN5, Q96DF8, Q9BRP8, Q9BSF4, Q9BYN8

Diamond homologs: O44424, O70279, P34420, Q96DF8, O59793

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 164 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
mRNA Splicing2323.2×2e-23
Processing of Capped Intron-Containing Pre-mRNA2518.8×3e-23
mRNA Splicing - Major Pathway3618.1×2e-33
Transport of Mature Transcript to Cytoplasm517.5×5e-04
mRNA 3’-end processing916.3×3e-07
RNA Polymerase II Transcription Termination816.1×2e-06
mRNA Polyadenylation1915.3×1e-15
mRNA Splicing - Minor Pathway714.4×3e-05

GO biological processes:

GO termPartnersFoldFDR
U2-type prespliceosome assembly834.7×1e-08
RNA splicing, via transesterification reactions626.0×1e-05
spliceosomal complex assembly625.1×2e-05
mRNA splicing, via spliceosome3220.4×3e-30
spliceosomal snRNP assembly520.2×4e-04
mRNA transport712.8×1e-04
RNA splicing2012.2×8e-14
regulation of alternative mRNA splicing, via spliceosome711.9×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance162
Likely benign13
Benign5

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
625622GRCh37/hg19 22q11.21(chr22:18923898-21431174)Pathogenic

SpliceAI

1814 predictions. Top by Δscore:

VariantEffectΔscore
22:19135054:CCTCA:Cdonor_loss1.0000
22:19135055:CTCA:Cdonor_loss1.0000
22:19135056:TCA:Tdonor_loss1.0000
22:19135057:CACCT:Cdonor_loss1.0000
22:19135058:ACCTG:Adonor_loss1.0000
22:19135093:T:TAdonor_gain1.0000
22:19135175:TCTA:Tacceptor_loss1.0000
22:19135176:C:CCacceptor_gain1.0000
22:19137318:CCCA:Cdonor_loss1.0000
22:19137319:CCAC:Cdonor_loss1.0000
22:19137320:CACCT:Cdonor_loss1.0000
22:19137321:A:AGdonor_loss1.0000
22:19137428:CACAC:Cacceptor_gain1.0000
22:19137429:ACAC:Aacceptor_gain1.0000
22:19137429:ACACC:Aacceptor_loss1.0000
22:19137430:CAC:Cacceptor_gain1.0000
22:19137430:CACC:Cacceptor_gain1.0000
22:19137431:AC:Aacceptor_gain1.0000
22:19137431:ACCT:Aacceptor_loss1.0000
22:19137432:CC:Cacceptor_gain1.0000
22:19137432:CCT:Cacceptor_loss1.0000
22:19137433:C:CCacceptor_gain1.0000
22:19137433:C:CGacceptor_loss1.0000
22:19137434:T:Cacceptor_loss1.0000
22:19137440:C:CTacceptor_gain1.0000
22:19137441:A:Tacceptor_gain1.0000
22:19139154:CTCA:Cdonor_loss1.0000
22:19139155:TCA:Tdonor_loss1.0000
22:19139156:CA:Cdonor_loss1.0000
22:19139290:CAC:Cacceptor_gain1.0000

AlphaMissense

3086 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:19135155:C:AR352S0.999
22:19135155:C:GR352S0.999
22:19137326:A:CF344L0.999
22:19137326:A:TF344L0.999
22:19137328:A:GF344L0.999
22:19137406:A:GW318R0.999
22:19137406:A:TW318R0.999
22:19142819:C:GA71P0.999
22:19142862:A:CF56L0.999
22:19142862:A:TF56L0.999
22:19142864:A:GF56L0.999
22:19142865:G:CF55L0.999
22:19142865:G:TF55L0.999
22:19142867:A:GF55L0.999
22:19142878:A:TI51N0.999
22:19135156:C:AR352M0.998
22:19135156:C:GR352T0.998
22:19139954:A:CS157R0.998
22:19139954:A:TS157R0.998
22:19139956:T:GS157R0.998
22:19142788:C:GR81P0.998
22:19142845:A:GL62P0.998
22:19142878:A:CI51S0.998
22:19135133:C:GA360P0.997
22:19135135:A:GM359T0.997
22:19135174:A:GI346T0.997
22:19137327:A:GF344S0.997
22:19137403:C:GG319R0.997
22:19137403:C:TG319R0.997
22:19137404:C:AW318C0.997

dbSNP variants (sampled 300 via entrez): RS1000008133 (22:19137016 A>G), RS1000245173 (22:19136199 T>C), RS1000322876 (22:19131568 C>G,T), RS1000493130 (22:19140826 A>C), RS1000822566 (22:19145436 G>C), RS1001020279 (22:19134948 C>T), RS1001107807 (22:19145200 A>G), RS1001266142 (22:19130079 A>C,G), RS1001344751 (22:19136328 T>A,C), RS1001564102 (22:19136090 A>G), RS1001705475 (22:19146424 T>A,C), RS1001731346 (22:19130450 A>G), RS1002259473 (22:19140840 T>C), RS1002423323 (22:19145541 G>A), RS1002641122 (22:19141045 G>A)

Disease associations

OMIM: gene MIM:601755 | disease phenotypes: MIM:608363

GenCC curated gene-disease

Mondo (1): chromosome 22q11.2 microduplication syndrome (MONDO:0012020)

Orphanet (1): 22q11.2 duplication syndrome (Orphanet:1727)

HPO phenotypes

39 total (30 of 39 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000175Cleft palate
HP:0000176Submucous cleft hard palate
HP:0000194Open mouth
HP:0000201Pierre-Robin sequence
HP:0000220Velopharyngeal insufficiency
HP:0000252Microcephaly
HP:0000278Retrognathia
HP:0000414Bulbous nose
HP:0000430Underdeveloped nasal alae
HP:0000581Blepharophimosis
HP:0000598Abnormality of the ear
HP:0000627Posterior embryotoxon
HP:0000712Emotional lability
HP:0000718Aggressive behavior
HP:0000829Hypoparathyroidism
HP:0001155Abnormality of the hand
HP:0001249Intellectual disability
HP:0001252Hypotonia
HP:0001328Specific learning disability
HP:0001537Umbilical hernia
HP:0001611Hypernasal speech
HP:0001629Ventricular septal defect
HP:0001636Tetralogy of Fallot
HP:0001883Talipes
HP:0002627Right aortic arch with mirror image branching
HP:0002719Recurrent infections
HP:0002901Hypocalcemia

GWAS associations

4 associations (top):

StudyTraitp-value
GCST009391_356Metabolite levels8.000000e-07
GCST009391_365Metabolite levels3.000000e-06
GCST009391_469Metabolite levels1.000000e-06
GCST009391_916Metabolite levels8.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0010434triacylglycerol 56:7 measurement
EFO:0010435triacylglycerol 56:8 measurement
EFO:0010442triacylglycerol 58:8 measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C567224Chromosome 22q11.2 Microduplication Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
cobaltous chlorideincreases expression1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
coumarinincreases phosphorylation1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediaminedecreases expression1
abrineincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
Arsenicincreases expression, affects cotreatment, increases abundance1
Atrazinedecreases expression1
Caffeineincreases phosphorylation1
Doxorubicinincreases expression1
Leaddecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Methyl Methanesulfonateincreases expression1
Quercetindecreases phosphorylation1
Seleniumincreases expression1
Smokedecreases expression1
Sulindacincreases expression1
Tetrachlorodibenzodioxindecreases expression1
Thiramincreases expression1
Urethaneincreases expression1
Valproic Aciddecreases expression1
Vitamin Eincreases expression1
Cyclosporineincreases expression1
tert-Butylhydroperoxideincreases expression1

Clinical trials (associated diseases)

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