ICE2

gene
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Also known as FLJ11896BRCC1

Summary

ICE2 (interactor of little elongation complex ELL subunit 2, HGNC:29885) is a protein-coding gene on chromosome 15q22.2, encoding Little elongation complex subunit 2 (Q659A1). Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III. It is a selective cancer dependency (DepMap: 53.6% of cell lines).

This gene encodes a protein component of the little elongation complex (LEC), which plays a role in small nuclear RNA (snRNA) transcription. The LEC regulates snRNA transcription by enhancing both RNA Polymerase II occupancy and transcriptional elongation. The encoded protein and other LEC components have been shown to localize to Cajal bodies, which are sites of ribonucleoprotein (RNP) complex assembly. Pseudogenes of this gene have been identified on chromosomes 3 and 4.

Source: NCBI Gene 79664 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 195 total — 1 pathogenic, 1 likely-pathogenic
  • Cancer dependency (DepMap): dependent in 53.6% of screened cell lines
  • MANE Select transcript: NM_024611

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29885
Approved symbolICE2
Nameinteractor of little elongation complex ELL subunit 2
Location15q22.2
Locus typegene with protein product
StatusApproved
AliasesFLJ11896, BRCC1
Ensembl geneENSG00000128915
Ensembl biotypeprotein_coding
OMIM610835
Entrez79664

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 16 protein_coding, 4 retained_intron, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000261520, ENST00000558121, ENST00000558181, ENST00000558451, ENST00000558512, ENST00000558654, ENST00000560072, ENST00000560406, ENST00000560520, ENST00000560668, ENST00000560895, ENST00000561087, ENST00000561114, ENST00000561124, ENST00000561144, ENST00000561328, ENST00000561446, ENST00000874574, ENST00000874575, ENST00000874576, ENST00000915338, ENST00000915339, ENST00000915340, ENST00000915341, ENST00000915342, ENST00000915343, ENST00000915344

RefSeq mRNA: 3 — MANE Select: NM_024611 NM_001018089, NM_001276385, NM_024611

CCDS: CCDS10176, CCDS61657

Canonical transcript exons

ENST00000261520 — 16 exons

ExonStartEnd
ENSE000012282836047900360479142
ENSE000012283146046806160468322
ENSE000014237566041960960423762
ENSE000034726756043614360436227
ENSE000034845696045360360453784
ENSE000035130966045532660455442
ENSE000035296376046659460466713
ENSE000035382376043193460431984
ENSE000035437796044884860449841
ENSE000036226326044241660442545
ENSE000036274946047606360476167
ENSE000036309706045500360455162
ENSE000036490706047793760478069
ENSE000036570786044797060448145
ENSE000036584716042842960428687
ENSE000036630676045665760456794

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 94.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.4520 / max 309.0581, expressed in 1775 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15032314.11971775
1503220.3323146

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
colonic epitheliumUBERON:000039794.18gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.64gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047393.30gold quality
ventricular zoneUBERON:000305393.26gold quality
adrenal tissueUBERON:001830392.04gold quality
ganglionic eminenceUBERON:000402391.96gold quality
calcaneal tendonUBERON:000370191.51gold quality
tendonUBERON:000004391.11gold quality
embryoUBERON:000092290.99gold quality
left ovaryUBERON:000211990.08gold quality
hindlimb stylopod muscleUBERON:000425289.97gold quality
secondary oocyteCL:000065589.94gold quality
oocyteCL:000002389.65gold quality
islet of LangerhansUBERON:000000689.60gold quality
right ovaryUBERON:000211889.59gold quality
right uterine tubeUBERON:000130289.22gold quality
ovaryUBERON:000099288.91gold quality
C1 segment of cervical spinal cordUBERON:000646988.71gold quality
right lobe of thyroid glandUBERON:000111988.55gold quality
nerveUBERON:000102188.52gold quality
tibial nerveUBERON:000132388.52gold quality
pituitary glandUBERON:000000788.51gold quality
monocyteCL:000057688.39gold quality
adenohypophysisUBERON:000219688.38gold quality
body of uterusUBERON:000985388.35gold quality
leukocyteCL:000073888.30gold quality
mononuclear cellCL:000084288.29gold quality
endocervixUBERON:000045888.23gold quality
bone marrow cellCL:000209288.15gold quality
body of pancreasUBERON:000115087.98gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9801yes6.80
E-MTAB-7303no126.75
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

134 targeting ICE2, 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-3613-3P100.0076.367965
HSA-MIR-3646100.0073.565283
HSA-MIR-5193100.0067.261744
HSA-MIR-3163100.0077.238605
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-223-3P99.9970.141140
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-1213699.9872.815713
HSA-MIR-806899.9873.852376
HSA-MIR-548N99.9871.944170
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-426799.9666.532368

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 53.6% of screened cell lines.

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioice2ENSDARG00000086670
mus_musculusIce2ENSMUSG00000032235
rattus_norvegicusIce2ENSRNOG00000010160

Protein

Protein identifiers

Little elongation complex subunit 2Q659A1 (reviewed: Q659A1)

Alternative names: Interactor of little elongator complex ELL subunit 2, NMDA receptor-regulated protein 2

All UniProt accessions (8): Q659A1, H0YK14, H0YK96, H0YK97, H0YL35, H0YMX6, H0YN09, H0YNU9

UniProt curated annotations — full annotation on UniProt →

Function. Component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III.

Subunit / interactions. Component of the little elongation complex (LEC), at least composed of ELL (ELL, ELL2 or ELL3), ZC3H8, ICE1 and ICE2. Interacts with ICE1 (via C-terminus domain). Interacts with ELL.

Subcellular location. Nucleus.

Tissue specificity. Expressed at low levels in lung and testis.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the ICE2 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q659A1-11yes
Q659A1-22

RefSeq proteins (3): NP_001018099, NP_001263314, NP_078887* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019535ICE2_CDomain

Pfam: PF10505

UniProt features (26 total): compositionally biased region 7, sequence conflict 7, region of interest 5, modified residue 4, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q659A1-F166.240.30

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 (4): 17, 326, 571, 573

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6807505RNA polymerase II transcribes snRNA genes

MSigDB gene sets: 135 (showing top): GOBP_TRANSCRIPTION_BY_RNA_POLYMERASE_III, GTGCCTT_MIR506, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CREB_Q3, YRTCANNRCGC_UNKNOWN, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, NUYTTEN_EZH2_TARGETS_DN, GOCC_CAJAL_BODY, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_EUCHROMATIN, GOCC_TRANSCRIPTION_ELONGATION_FACTOR_COMPLEX, BENPORATH_ES_1, HAMAI_APOPTOSIS_VIA_TRAIL_UP

GO Biological Process (3): snRNA transcription by RNA polymerase II (GO:0042795), snRNA transcription by RNA polymerase III (GO:0042796), positive regulation of transcription by RNA polymerase III (GO:0045945)

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

GO Cellular Component (8): euchromatin (GO:0000791), nucleoplasm (GO:0005654), cytosol (GO:0005829), transcription elongation factor complex (GO:0008023), Cajal body (GO:0015030), nuclear body (GO:0016604), histone locus body (GO:0035363), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
snRNA transcription2
transcription by RNA polymerase III2
cellular anatomical structure2
nucleoplasm2
nuclear ribonucleoprotein granule2
transcription by RNA polymerase II1
regulation of transcription by RNA polymerase III1
positive regulation of DNA-templated transcription1
binding1
chromatin1
nuclear lumen1
cytoplasm1
nuclear protein-containing complex1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1184 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ICE2ICE1Q9Y2F5985
ICE2ZNF346Q9UL40947
ICE2NAA15Q9BXJ9940
ICE2ZC3H8Q8N5P1834
ICE2NAA10P41227763
ICE2ELLP55199750
ICE2GRIN1P35437648
ICE2USPL1Q5W0Q7591
ICE2MNAT1P51948581
ICE2MED26O95402514
ICE2EAF1Q96JC9504
ICE2NAT1P18440474
ICE2EAF2Q96CJ1457
ICE2ELL2O00472434
ICE2ELL3Q9HB65425

IntAct

60 interactions, top by confidence:

ABTypeScore
EAF1ELL2psi-mi:“MI:0914”(association)0.840
ELL3ICE2psi-mi:“MI:0914”(association)0.730
ELL3CCNT1psi-mi:“MI:0914”(association)0.640
SNRPA1HTATSF1psi-mi:“MI:0914”(association)0.640
SNRPA1U2SURPpsi-mi:“MI:0914”(association)0.640
SNRPBSART1psi-mi:“MI:0914”(association)0.640
ICE1ELLpsi-mi:“MI:0915”(physical association)0.620
ICE2ELLpsi-mi:“MI:0915”(physical association)0.620
ELLICE2psi-mi:“MI:0914”(association)0.620
ICE2ELLpsi-mi:“MI:0914”(association)0.620
ICE1ELLpsi-mi:“MI:0914”(association)0.620
ICE2HPpsi-mi:“MI:0914”(association)0.530
DYRK1BBMAL1psi-mi:“MI:0914”(association)0.530
Ncbp2ZC3H18psi-mi:“MI:0914”(association)0.350
OFD1CCDC14psi-mi:“MI:0914”(association)0.350
Ankrd26TBC1D31psi-mi:“MI:0914”(association)0.350
ScaiBCRpsi-mi:“MI:0914”(association)0.350
OsgepRPSApsi-mi:“MI:0914”(association)0.350
FGFR1OP2STK24psi-mi:“MI:0914”(association)0.350
SIKE1STK24psi-mi:“MI:0914”(association)0.350

BioGRID (112): ICE2 (Affinity Capture-MS), ICE2 (Affinity Capture-MS), ICE2 (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), IGKC (Affinity Capture-MS), IGLC7 (Affinity Capture-MS), IGHG2 (Affinity Capture-MS), IGHG1 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), PIGR (Affinity Capture-MS), HP (Affinity Capture-MS), LTF (Affinity Capture-MS), MUC5B (Affinity Capture-MS), SERPINA1 (Affinity Capture-MS), BPIFA1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A4D1B5, A4FUB0, D3IUT5, D3Z6S9, F1QB81, O60281, O70167, P53995, Q0VCQ7, Q13129, Q14699, Q2T9I9, Q3TCV3, Q3UJC8, Q402B2, Q4R9E9, Q5RA75, Q5RB52, Q5XI46, Q5XI56, Q5ZKI7, Q659A1, Q6AYM1, Q6DRL4, Q6INI0, Q6PUR7, Q7Z2Z1, Q8BQ33, Q8CCC3, Q8CDN1, Q8IXR9, Q8K1K4, Q8NB91, Q8ND61, Q90WN7, Q920I9, Q92674

Diamond homologs: Q0VCQ7, Q3UZ18, Q659A1

SIGNOR signaling

1 interactions.

AEffectBMechanism
ICE2“form complex”ELL/ICE2binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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
RNA polymerase II transcribes snRNA genes621.5×7e-05
mRNA Splicing615.3×2e-04
CHD1 and CHD2 subfamily512.7×2e-03
mRNA Polyadenylation612.3×4e-04
Processing of Capped Intron-Containing Pre-mRNA611.5×5e-04
mRNA Splicing - Major Pathway810.2×1e-04
Metabolism of RNA76.8×2e-03
Dengue Virus-Host Interactions66.4×7e-03

GO biological processes:

GO termPartnersFoldFDR
U2-type prespliceosome assembly555.7×4e-06
positive regulation of transcription elongation by RNA polymerase II632.2×4e-06
mRNA splicing, via spliceosome711.4×2e-04
RNA splicing69.4×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance147
Likely benign17
Benign5

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
4820238Single allelePathogenic
2685518GRCh37/hg19 15q22.2(chr15:60688155-60888244)x1Likely pathogenic

SpliceAI

3427 predictions. Top by Δscore:

VariantEffectΔscore
15:60436141:A:ACdonor_gain1.0000
15:60436142:C:CCdonor_gain1.0000
15:60436224:TGCC:Tacceptor_gain1.0000
15:60436226:CC:Cacceptor_gain1.0000
15:60436227:CC:Cacceptor_gain1.0000
15:60436227:CCTA:Cacceptor_loss1.0000
15:60436228:C:CCacceptor_gain1.0000
15:60436228:CTA:Cacceptor_loss1.0000
15:60436229:T:Aacceptor_loss1.0000
15:60449843:T:Cacceptor_gain1.0000
15:60449845:A:ACacceptor_gain1.0000
15:60449845:A:Cacceptor_gain1.0000
15:60453601:A:ACdonor_gain1.0000
15:60453601:ACGT:Adonor_gain1.0000
15:60453602:C:CCdonor_gain1.0000
15:60453602:CGT:Cdonor_gain1.0000
15:60453602:CGTC:Cdonor_gain1.0000
15:60453604:T:TAdonor_gain1.0000
15:60453605:C:Adonor_gain1.0000
15:60453786:T:Cacceptor_gain1.0000
15:60455320:ACTT:Adonor_loss1.0000
15:60455322:TTACA:Tdonor_loss1.0000
15:60455323:TA:Tdonor_loss1.0000
15:60455324:A:ACdonor_gain1.0000
15:60455324:A:Cdonor_loss1.0000
15:60455325:C:CTdonor_gain1.0000
15:60455325:CA:Cdonor_gain1.0000
15:60455325:CAT:Cdonor_gain1.0000
15:60455325:CATA:Cdonor_gain1.0000
15:60455325:CATAA:Cdonor_gain1.0000

AlphaMissense

6448 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:60449021:A:GL649S0.999
15:60449024:A:CI648S0.999
15:60449024:A:GI648T0.999
15:60449033:A:TV645D0.999
15:60449003:A:GL655P0.998
15:60449015:A:GM651T0.998
15:60428533:A:GW906R0.997
15:60428533:A:TW906R0.997
15:60449024:A:TI648N0.997
15:60428465:A:CF928L0.996
15:60428465:A:TF928L0.996
15:60428467:A:GF928L0.996
15:60447970:T:AR765S0.996
15:60447970:T:GR765S0.996
15:60449011:C:AQ652H0.996
15:60449011:C:GQ652H0.996
15:60449039:T:CD643G0.996
15:60442535:A:TV769D0.995
15:60455042:A:GW302R0.995
15:60455042:A:TW302R0.995
15:60466675:G:CF149L0.995
15:60466675:G:TF149L0.995
15:60466677:A:GF149L0.995
15:60442416:C:GG809R0.994
15:60442416:C:TG809R0.994
15:60447973:T:AR764S0.994
15:60447973:T:GR764S0.994
15:60448071:A:CY732D0.994
15:60455131:A:GL272P0.994
15:60436227:C:TG809E0.993

dbSNP variants (sampled 300 via entrez): RS1000023766 (15:60451528 T>C), RS1000054552 (15:60465202 C>A,T), RS1000086576 (15:60479325 G>A,C), RS1000093034 (15:60441197 A>G), RS1000167256 (15:60471813 A>G), RS1000227119 (15:60430135 A>G), RS1000258485 (15:60433979 C>G), RS1000283296 (15:60433656 A>G), RS1000288579 (15:60438702 G>A), RS1000340326 (15:60438287 A>G), RS1000481988 (15:60444549 T>A), RS1000494330 (15:60457056 G>A,C), RS1000512542 (15:60472813 C>A), RS1000543619 (15:60472620 T>C), RS1000586430 (15:60433013 T>A,C)

Disease associations

OMIM: gene MIM:610835 | disease phenotypes: MIM:618060

GenCC curated gene-disease

Mondo (1): intellectual developmental disorder with or without epilepsy or cerebellar ataxia (MONDO:0060745)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST005212_29Asthma1.000000e-09
GCST006862_16Asthma8.000000e-11
GCST009391_1441Metabolite levels3.000000e-06
GCST009391_1845Metabolite levels3.000000e-06
GCST009798_17Asthma2.000000e-19
GCST90002381_617Eosinophil count4.000000e-09
GCST90002382_236Eosinophil percentage of white cells7.000000e-12

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0010409triacylglycerol 50:2 measurement
EFO:0010413triacylglycerol 52:1 measurement
EFO:0004842eosinophil count
EFO:0007991eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression6
Arsenicaffects methylation, increases methylation, affects cotreatment, decreases expression, increases abundance3
sodium arsenitedecreases expression, affects cotreatment, increases abundance2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
FR900359increases phosphorylation1
dicrotophosdecreases expression1
geldanamycinincreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
testosterone undecanoateaffects cotreatment, decreases expression1
beta-lapachoneincreases expression1
butyraldehydedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
coumarindecreases phosphorylation1
lei gong tengincreases expression1
epigallocatechin gallateincreases expression1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
belinostatincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression, increases response to substance1
jinfukangdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Acetaminophenincreases expression1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Cadmiumincreases abundance, increases expression1
Caffeineincreases phosphorylation1

Clinical trials (associated diseases)

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