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CELF4

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Summary

CELF4 (CUGBP Elav-like family member 4, HGNC:14015) is a protein-coding gene on chromosome 18q12.2, encoding CUGBP Elav-like family member 4 (Q9BZC1). RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing.

Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 56853 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Definitive, GenCC) — +1 more curated relationship
  • GWAS associations: 36 (top 3% of genes corpus-wide)
  • Clinical variants (ClinVar): 122 total — 1 pathogenic
  • Regional missense constraint (gnomAD): 3 of 7 regions constrained (≈11% of expected missense variation)
  • GTEx eGene: eQTL in 24 tissues, sQTL in 1 (q < 0.05)
  • Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
  • Constraint (gnomAD): pLI 0.84 (intermediate), LOEUF 0.55 (moderately constrained)
  • MANE Select transcript: NM_020180

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14015
Approved symbolCELF4
NameCUGBP Elav-like family member 4
Location18q12.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000101489
Ensembl biotypeprotein_coding
OMIM612679
Entrez56853

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 46 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

MANE Select: ENST00000420428

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 6, TSL 2: 5, TSL 3: 8, TSL 4: 1, TSL 5: 3

ENST00000420428, ENST00000334919, ENST00000361795, ENST00000586009, ENST00000587074, ENST00000587449, ENST00000587657, ENST00000587819, ENST00000587911, ENST00000587924, ENST00000588591, ENST00000588597, ENST00000589229, ENST00000589386, ENST00000590011, ENST00000590112, ENST00000591282, ENST00000591287, ENST00000591421, ENST00000593271, ENST00000601019, ENST00000601392, ENST00000603232, ENST00000899355, ENST00000899356, ENST00000899357, ENST00000899358, ENST00000899359, ENST00000899360, ENST00000899361, ENST00000899362, ENST00000899363, ENST00000899364, ENST00000899365, ENST00000931906, ENST00000970536, ENST00000970537, ENST00000970538, ENST00000970539, ENST00000970540, ENST00000970541, ENST00000970542, ENST00000970543, ENST00000970544, ENST00000970545, ENST00000970546, ENST00001009546, ENST00001009547, ENST00001009548, ENST00001009549, ENST00001098493, ENST00001131485

RefSeq mRNA: 70 — MANE Select: NM_020180 NM_001025087, NM_001025088, NM_001025089, NM_001330603, NM_001353695, NM_001353696, NM_001353697, NM_001353698, NM_001353699, NM_001353700, NM_001353702, NM_001353703, NM_001353705, NM_001353706, NM_001353707, NM_001353708, NM_001353709, NM_001353710, NM_001353711, NM_001353712, NM_001353713, NM_001353714, NM_001353715, NM_001353716, NM_001353717, NM_001353718, NM_001353719, NM_001353720, NM_001353721, NM_001353722, NM_001353723, NM_001353724, NM_001353725, NM_001353726, NM_001353727, NM_001353728, NM_001353729, NM_001353730, NM_001353731, NM_001353732, NM_001353733, NM_001353734, NM_001353735, NM_001353736, NM_001353737, NM_001353738, NM_001353739, NM_001353740, NM_001353741, NM_001353742, NM_001353743, NM_001353744, NM_001353745, NM_001353746, NM_001353747, NM_001353748, NM_001353749, NM_001353750, NM_001353751, NM_001353752, NM_001353753, NM_001353754, NM_001353755, NM_001353756, NM_001353757, NM_001353758, NM_001353759, NM_001353760, NM_001353761, NM_020180

CCDS: CCDS32818, CCDS45856, CCDS45857, CCDS45858, CCDS82250

Canonical transcript exons

ENST00000420428 — 13 exons

ExonStartEnd
ENSE000027256043756535637565798
ENSE000034693103748552537485607
ENSE000034757413726653337266598
ENSE000034853443725918137259264
ENSE000035064643727076837270917
ENSE000035698983727301637273163
ENSE000036322963726467437264757
ENSE000036580673725376737253938
ENSE000038473713724304037245197
ENSE000038893513727511537275243
ENSE000038893873727431137274454
ENSE000038919073732180337321881
ENSE000038922083727480537274884

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 97.29.

FANTOM5 (CAGE): breadth broad, TPM avg 5.0549 / max 1047.8138, expressed in 310 samples.

Highest expression (Bgee): cerebellar cortex, cerebellar hemisphere, Brodmann (1909) area 9, hemisphere of cerebellum, primary visual cortex.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CELF4 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 24 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 25 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Nerve Tibialeqtl2.7e-29-0.6718:36949475:A:C
Testissqtl2.6e-22+0.9618:37322162:T:G
Skin Sun Exposed Lower legeqtl2.0e-20-0.6018:36995714:G:T
Skin Not Sun Exposed Suprapubiceqtl4.0e-13-0.5418:36949475:A:C
Esophagus Mucosaeqtl2.0e-12-0.5918:36879775:G:A
Thyroideqtl4.5e-12+0.4618:36923067:C:T
Artery Tibialeqtl2.0e-10-0.4518:37103271:G:T
Breast Mammary Tissueeqtl4.7e-08-0.4218:36848399:A:T
Adipose Subcutaneouseqtl8.5e-08-0.3818:37229747:G:A
Esophagus Musculariseqtl3.7e-06-0.2118:37162663:C:T
Colon Transverseeqtl5.1e-05-0.1518:37252704:G:A
Artery Aortaeqtl6.2e-05-0.3618:37258244:C:T
Muscle Skeletaleqtl3.4e-04-0.2918:37216697:G:C
Small Intestine Terminal Ileumeqtl5.4e-04-0.3618:37166595:T:G
Brain Hippocampuseqtl6.9e-04+0.3718:37707164:A:G
Ovaryeqtl1.3e-03-0.4418:37192536:A:G
Brain Cortexeqtl1.4e-03-0.1518:37251003:A:G
Artery Coronaryeqtl1.4e-03-0.4818:37261740:G:T
Vaginaeqtl1.9e-03-0.4318:37223202:A:G
Lungeqtl3.2e-03-0.2818:37252704:G:A

FANTOM5 promoters

showing 10 of 11 alternative TSS:

Promoter IDTPM avgSamples expressed
1717232.6440137
1717220.7488103
1717050.3728137
1717250.3664104
1717200.299088
1717120.178192
1717130.167661
1717210.131660
1717240.065739
1717180.042931

Top tissues by expression

showing 100 of 252 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212997.29gold quality
cerebellar hemisphereUBERON:000224597.28gold quality
Brodmann (1909) area 9UBERON:001354097.15gold quality
right hemisphere of cerebellumUBERON:001489097.08gold quality
primary visual cortexUBERON:000243697.01gold quality
cerebellumUBERON:000203796.93gold quality
dorsolateral prefrontal cortexUBERON:000983496.66gold quality
Brodmann (1909) area 23UBERON:001355496.55gold quality
right frontal lobeUBERON:000281096.50gold quality
anterior cingulate cortexUBERON:000983596.40gold quality
prefrontal cortexUBERON:000045196.35gold quality
frontal cortexUBERON:000187096.21gold quality
neocortexUBERON:000195095.87gold quality
superior frontal gyrusUBERON:000266195.83gold quality
occipital lobeUBERON:000202195.66gold quality
nucleus accumbensUBERON:000188295.58gold quality
cerebral cortexUBERON:000095695.43gold quality
entorhinal cortexUBERON:000272895.33gold quality
amygdalaUBERON:000187695.29gold quality
hypothalamusUBERON:000189895.29gold quality
temporal lobeUBERON:000187195.16gold quality
cerebellar vermisUBERON:000472095.14gold quality
postcentral gyrusUBERON:000258194.60gold quality
substantia nigra pars compactaUBERON:000196594.53gold quality
parietal lobeUBERON:000187294.46gold quality
Brodmann (1909) area 46UBERON:000648394.39gold quality
middle temporal gyrusUBERON:000277194.36gold quality
brainUBERON:000095594.01gold quality
forebrainUBERON:000189093.99gold quality
Ammon’s hornUBERON:000195493.77gold quality
caudate nucleusUBERON:000187393.07gold quality
cortical plateUBERON:000534392.90gold quality
putamenUBERON:000187492.85gold quality
substantia nigra pars reticulataUBERON:000196692.75gold quality
ponsUBERON:000098892.21gold quality
superior vestibular nucleusUBERON:000722791.67gold quality
ventral tegmental areaUBERON:000269190.53gold quality
adenohypophysisUBERON:000219690.46gold quality
lateral nuclear group of thalamusUBERON:000273690.30gold quality
substantia nigraUBERON:000203890.18gold quality
midbrainUBERON:000189190.08gold quality
pituitary glandUBERON:000000790.03gold quality
endothelial cellCL:000011587.77gold quality
medulla oblongataUBERON:000189687.14gold quality
buccal mucosa cellCL:000233686.19gold quality
dorsal root ganglionUBERON:000004483.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.53gold quality
ganglionic eminenceUBERON:000402380.11gold quality
lateral globus pallidusUBERON:000247679.06gold quality
islet of LangerhansUBERON:000000678.80gold quality
C1 segment of cervical spinal cordUBERON:000646978.74gold quality
spinal cordUBERON:000224078.09gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099177.77gold quality
dorsal plus ventral thalamusUBERON:000189777.40gold quality
pancreatic ductal cellCL:000207976.02silver quality
sural nerveUBERON:001548875.86gold quality
ventricular zoneUBERON:000305374.06gold quality
globus pallidusUBERON:000187573.17gold quality
medial globus pallidusUBERON:000247772.32gold quality
pancreasUBERON:000126471.72gold quality
body of pancreasUBERON:000115069.40gold quality
adult organismUBERON:000702369.35silver quality
left testisUBERON:000453369.20gold quality
right testisUBERON:000453468.57gold quality
testisUBERON:000047367.66gold quality
corpus callosumUBERON:000233666.95gold quality
subthalamic nucleusUBERON:000190666.34gold quality
body of stomachUBERON:000116166.21gold quality
gall bladderUBERON:000211066.10gold quality
trigeminal ganglionUBERON:000167565.94gold quality
muscle layer of sigmoid colonUBERON:003580565.34gold quality
stomachUBERON:000094564.39gold quality
tendon of biceps brachiiUBERON:000818864.05gold quality
left ovaryUBERON:000211963.50gold quality
colonic epitheliumUBERON:000039763.44gold quality
vermiform appendixUBERON:000115462.77gold quality
anatomical systemUBERON:000046761.77gold quality
parotid glandUBERON:000183161.71gold quality
fundus of stomachUBERON:000116061.67gold quality
hindlimb stylopod muscleUBERON:000425261.65gold quality
apex of heartUBERON:000209861.59gold quality
multicellular organismUBERON:000046861.42gold quality
right adrenal glandUBERON:000123361.42gold quality
material anatomical entityUBERON:000046561.40gold quality
adrenal glandUBERON:000236961.17gold quality
tibialis anteriorUBERON:000138560.99silver quality
cortex of kidneyUBERON:000122560.70gold quality
right ovaryUBERON:000211860.48gold quality
left adrenal gland cortexUBERON:003582560.43gold quality
left adrenal glandUBERON:000123460.03gold quality
right atrium auricular regionUBERON:000663159.63gold quality
ovaryUBERON:000099259.18gold quality
cardiac atriumUBERON:000208159.05gold quality
adrenal cortexUBERON:000123559.00gold quality
oviduct epitheliumUBERON:000480458.79silver quality
lower esophagus muscularis layerUBERON:003583358.62gold quality
lower esophagusUBERON:001347358.48gold quality
adrenal tissueUBERON:001830358.48gold quality
esophagogastric junction muscularis propriaUBERON:003584158.06gold quality
metanephros cortexUBERON:001053357.89gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 10.

ExperimentMarker?Max mean expression
E-MTAB-7316yes954.02
E-MTAB-11121yes690.43
E-HCAD-5yes519.48
E-GEOD-75140yes90.69
E-HCAD-35yes63.73
E-HCAD-25yes36.94
E-GEOD-93593yes16.57
E-GEOD-137537yes11.04
E-GEOD-84465yes7.06
E-ANND-3yes4.07

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 75 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Postcentral gyrustissue235.2
Frontal cortextissue230.9
Hippocampustissue147.3low
Caudate putamentissue146.4
Locus coeruleustissue143.4
Nucleus accumbenstissue94.2
Prefrontal cortextissue92.4
Cerebral cortextissue92.4medium
Cerebellumtissue92.0low
Basal gangliatissue87.0medium
Hippocampal formationtissue85.5
Motor cortextissue85.4
Olfactory bulbtissue84.7
Retrosplenial cortextissue79.6
Retrosplenial and cingulate cortextissue79.4
Insular cortextissue78.8
Entorhinal cortextissue78.3
Putamentissue77.6
Ventral forebraintissue74.5
Occipital cortextissue72.4
Somatosensory cortextissue72.2
Amygdalatissue71.0
Temporal cortextissue70.3
Septumtissue69.3
Ponstissue67.5
Hypothalamustissue64.7
Thalamustissue61.5
Midbraintissue53.6
Substantia nigratissue52.9
Periaqueductal graytissue46.6
Superior colliculitissue40.4
Medulla oblongatatissue29.1
Pituitary glandtissue26.9
Retinatissue19.8
Spinal cordtissue18.2
Corpus callosumtissue17.6
Choroid plexustissue13.5
Adrenal glandtissue10.8not detected
Skeletal muscletissue10.2not detected
Pancreastissue3.7not detected
Testistissue3.4not detected
Salivary glandtissue1.6not detected
Thyroid glandtissue1.4not detected
Skin 1tissue1.2not detected
Small intestinetissue1.2not detected
Gallbladdertissue1.2not detected
Heart muscletissue1.0not detected
Spleentissue1.0not detected
Appendixtissue1.0not detected
Lymph nodetissue0.8not detected
Stomach 1tissue0.8not detected
Placentatissue0.8not detected
Ovarytissue0.7not detected
Colontissue0.7not detected
Duodenumtissue0.7not detected
Prostatetissue0.7not detected
Adipose tissuetissue0.6not detected
Kidneytissue0.6not detected
Esophagustissue0.5not detected
Smooth muscletissue0.5not detected

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Olfactory area (212.2), Olfactory tubercle (208.0), Stria terminalis, bed nucleus (205.2), Posterior insular cortex (204.7), Perirhinal gyrus (191.2).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CELF4 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 145 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-574-5P100.0066.01989
HSA-MIR-12118100.0065.881270
HSA-MIR-4682100.0068.891258
HSA-MIR-5692A100.0074.406850
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-318599.9968.121959
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-477599.9875.006394
HSA-MIR-1213699.9872.815713
HSA-MIR-569699.9872.364487
HSA-MIR-548N99.9871.944170
HSA-MIR-3065-5P99.9771.563281

Functional genomics

gnomAD constraint: pLI 0.836, LOEUF 0.546, missense Z 2.88 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000420428 splits into 7 regions with different missense tolerance; 3 are missense-constrained (≈11% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
18:37,253,814–37,274,378256 / 340.80.75no
18:37,274,379–37,274,4356 / 29.60.20yes (p 1.4e-05)
18:37,274,436–37,275,20156 / 92.00.61no
18:37,275,202–37,321,8081 / 18.60.05yes (p 4.5e-05)
18:37,321,809–37,565,42963 / 110.60.57no
18:37,565,430–37,565,4934 / 27.80.14yes (p 6.5e-06)
18:37,565,494–37,565,64170 / 69.51.01no
ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

  • Determination of CELF4 protein domains required for RNA splicing. (PMID:14973222)
  • validated occurrence of an unusual TG 3’ splice site in intron 6 (PMID:17672918)
  • Authors report a modifying effect of a polymorphism of CELF4 on the dose-dependent association between anthracyclines and cardiomyopathy, which possibly occurs through a pathway that involves the expression of abnormally spliced TNNT2 variants. (PMID:26811534)
  • The present study refines the molecular and neuropsychiatric phenotype associated with 18q12.2 deletion leading to CELF4 haploinsufficiency and provides evidence for a role for CELF4 in brain development and autism spectrum disorders. (PMID:28407444)
  • An intronic variant in the CELF4 gene is associated with risk for colorectal cancer. (PMID:33930674)
  • Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex. (PMID:37758766)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_reriocelf4ENSDARG00000070045
mus_musculusCelf4ENSMUSG00000024268
rattus_norvegicusCelf4ENSRNOG00000014503
drosophila_melanogasterbru1FBGN0000114
drosophila_melanogasterPofFBGN0035047
drosophila_melanogasterbru2FBGN0262475
caenorhabditis_elegansWBGENE00017135
caenorhabditis_elegansWBGENE00017140
caenorhabditis_elegansWBGENE00020354

Paralogs (6): CELF2 (ENSG00000048740), RBM28 (ENSG00000106344), CELF6 (ENSG00000140488), CELF1 (ENSG00000149187), CELF3 (ENSG00000159409), CELF5 (ENSG00000161082)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1932407) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 29 distinct phenotype terms.

Mouse phenotype (MP)Records
decreased body size2
seizures2
absence seizures2
tonic-clonic seizures2
increased susceptibility to induction of seizure by inducing agent2
decreased circulating calcium level1
convulsive seizures1
increased body weight1
hyperactivity1
abnormal seizure response to electrical stimulation1
increased circulating insulin level1
premature death1
abnormal bile duct morphology1
abnormal eye muscle morphology1
fetal growth retardation1
abnormal miniature excitatory postsynaptic currents1
decreased circulating cholesterol level1
impaired glucose tolerance1
increased susceptibility to weight gain1
abnormal spike wave discharge1
postnatal lethality, incomplete penetrance1
neonatal lethality, incomplete penetrance1
preweaning lethality, complete penetrance1
dual inferior vena cava1
decreased susceptibility to induction of seizure by inducing agent1

+4 more (showing top 25).

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Pongo abeliiQ5NVC8100.0%Diamond
Gallus gallusQ7T2T199.8%Diamond
Oryza sativa Indica GroupB8BCZ899.5%Diamond
Oryza sativa Japonica GroupQ6K27199.5%Diamond
Bos taurusQ08E0798.3%Diamond
Macaca fascicularisQ4R53597.5%Diamond
Xenopus tropicalisA4IIM296.8%Diamond
Xenopus laevisQ7ZXE296.8%Diamond
Canis lupus familiarisQ9XSR393.8%Diamond
Arabidopsis thalianaQ9ZW3692.1%Diamond
Musca domesticaO1731090.6%Diamond
Chrysomya rufifaciesO9701890.6%Diamond
Plasmodium falciparumP1382465.7%Diamond
Saccharomyces cerevisiae S288CQ0091646.2%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
SNORA111snoRNA106635546
KIAA1328protein-coding57536
TPGS2protein-coding25941
FHOD3protein-coding80206
MIR4318ncRNA100422857

Protein

Protein identifiers

CUGBP Elav-like family member 4 — Q9BZC1 (reviewed: Q9BZC1)

Alternative names: Bruno-like protein 4, CUG-BP- and ETR-3-like factor 4, RNA-binding protein BRUNOL-4

All UniProt accessions (14): A0A0A0MTT3, A0A0C4DGR1, B4DHA8, Q9BZC1, K7EJ26, K7EJD7, K7EJK3, K7EJW4, K7ENR2, K7EPX2, K7EQ97, K7ERH1, M0QY66, M0R137

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Promotes exclusion of both the smooth muscle (SM) and non-muscle (NM) exons in actinin pre-mRNAs. Activates the splicing of MAPT/Tau exon 10. Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitous. Strongly expressed in the cerebellum, hippocampus, amygdala, temporal and frontal cortex and frontal lobes.

Similarity. Belongs to the CELF/BRUNOL family.

Isoforms (5)

UniProt IDNamesCanonical?
Q9BZC1-11yes
Q9BZC1-22
Q9BZC1-33
Q9BZC1-44
Q9BZC1-55

RefSeq proteins (70): NP_001020258, NP_001020259, NP_001020260, NP_001317532, NP_001340624, NP_001340625, NP_001340626, NP_001340627, NP_001340628, NP_001340629, NP_001340631, NP_001340632, NP_001340634, NP_001340635, NP_001340636, NP_001340637, NP_001340638, NP_001340639, NP_001340640, NP_001340641, NP_001340642, NP_001340643, NP_001340644, NP_001340645, NP_001340646, NP_001340647, NP_001340648, NP_001340649, NP_001340650, NP_001340651, NP_001340652, NP_001340653, NP_001340654, NP_001340655, NP_001340656, NP_001340657, NP_001340658, NP_001340659, NP_001340660, NP_001340661, NP_001340662, NP_001340663, NP_001340664, NP_001340665, NP_001340666, NP_001340667, NP_001340668, NP_001340669, NP_001340670, NP_001340671, NP_001340672, NP_001340673, NP_001340674, NP_001340675, NP_001340676, NP_001340677, NP_001340678, NP_001340679, NP_001340680, NP_001340681, NP_001340682, NP_001340683, NP_001340684, NP_001340685, NP_001340686, NP_001340687, NP_001340688, NP_001340689, NP_001340690, NP_064565* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000504RRM_domDomain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR034648CELF3/4/5/6_RRM1Domain
IPR035979RBD_domain_sfHomologous_superfamily

Pfam: PF00076

UniProt features (35 total): strand 9, splice variant 5, sequence conflict 4, helix 4, region of interest 4, domain 3, turn 2, compositionally biased region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures by resolution:

PDBTitleMethodResolution (Å)
2DGPSolution structure of the N-terminal RNA binding domain in Bruno-like 4 RNA-binding …SOLUTION NMR
2DNKSolution structure of RNA binding domain in Bruno-like 4 RNA binding proteinSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BZC1-F162.700.23

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF supported

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 278 (showing top): GGGACCA_MIR133A_MIR133B, RNGTGGGC_UNKNOWN, RRAGTTGT_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, HNF3ALPHA_Q6, GOBP_POSITIVE_REGULATION_OF_RNA_SPLICING, GOBP_POSITIVE_REGULATION_OF_MRNA_PROCESSING, GCANCTGNY_MYOD_Q6, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MEF2_02, GGGTGGRR_PAX4_03, GCGCTTT_MIR518B_MIR518C_MIR518D

GO Biological Process (10): alternative mRNA splicing, via spliceosome (GO:0000380), regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA splice site recognition (GO:0006376), germ cell development (GO:0007281), embryo development ending in birth or egg hatching (GO:0009792), positive regulation of mRNA splicing, via spliceosome (GO:0048026), mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380), negative regulation of translation (GO:0017148)

GO Molecular Function (7): mRNA regulatory element binding translation repressor activity (GO:0000900), mRNA binding (GO:0003729), pre-mRNA binding (GO:0036002), BRE binding (GO:0042835), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), ribonucleoprotein complex (GO:1990904)

GO top-level categories

31 GO namespaces:

CategoryTerms
RNA binding3
mRNA splicing, via spliceosome2
regulation of mRNA splicing, via spliceosome2
RNA processing2
binding2
cellular anatomical structure2
alternative mRNA splicing, via spliceosome1
spliceosomal complex assembly1
protein-RNA complex assembly1
developmental process involved in reproduction1
gamete generation1
cellular process involved in reproduction in multicellular organism1
cell development1
embryo development1
animal gross anatomical part developmental process1
positive regulation of RNA splicing1
positive regulation of mRNA processing1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA metabolic process1
translation1
regulation of translation1
negative regulation of gene expression1
negative regulation of protein metabolic process1
mRNA binding1
translation repressor activity1
nucleic acid binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
protein-containing complex1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 6 of 21 annotations. The rest are phylogenetic / computational / electronic (IEA).

6 experimentally-supported GO terms:

GO termNSEvidence
alternative mRNA splicing, via spliceosomeBPdirect assay
positive regulation of mRNA splicing, via spliceosomeBPdirect assay
regulation of alternative mRNA splicing, via spliceosomeBPdirect assay
nucleoplasmCCdirect assay
nucleusCCdirect assay
pre-mRNA bindingMFdirect assay

Protein interactions and networks

STRING

showing 15 of 964 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
CELF4CEBPDP49716881
CELF4BICD1Q96G01837
CELF4DDX11Q96FC9759
CELF4TNNT2P45379698
CELF4PLEKHB2Q96CS7592
CELF4RBFOX1Q9NWB1532
CELF4MBNL2Q5VZF2515
CELF4MBNL1Q9NR56488
CELF4MBNL3Q9NUK0485
CELF4SRSF6Q13247477
CELF4SRSF4Q08170455
CELF4RBFOX2O43251446
CELF4CLCN1P35523443
CELF4SRSF9Q13242435
CELF4SLC28A3Q9HAS3419

IntAct

BioGRID (14 interactions; top human partners by supporting records): APP (Reconstituted Complex), AUP1 (Affinity Capture-MS), LPCAT1 (Affinity Capture-MS), LYST (Two-hybrid), MSI2 (Affinity Capture-MS), PCBP3 (Two-hybrid), POLI (Reconstituted Complex), PRR20A (Two-hybrid), PRR20B (Two-hybrid), PRR20C (Two-hybrid), PRR20D (Two-hybrid), PRR20E (Two-hybrid), RBPMS2 (Two-hybrid), TIAL1 (Two-hybrid)

SIGNOR signaling

2 signaling interactions:

AEffectBMechanism
CELF4“up-regulates quantity”TNNT2“post transcriptional regulation”
CELF4up-regulatesExcitatory_synaptic_transmission

Disease & clinical

Genetic variants

Variant evidence for CELF4: 122 ClinVar records (1 pathogenic / likely pathogenic); 1 PharmGKB clinical annotation; 36 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance89
Likely benign17
Benign6

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
3774946NM_020180.4(CELF4):c.226G>T (p.Glu76Ter)Pathogeniccriteria provided, single submitter1

Per-variant reference — Sugi Variant

Explore CELF4’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 35 predictions of 1,678):

Position(s)EffectΔscoreSites
18:37253765–37253766donor_loss1.00004
18:37264811acceptor_gain1.0000
18:37270930acceptor_gain1.0000
18:37273014–37273015donor_loss1.00005
18:37273164–37273165acceptor_loss1.00005
18:37273171acceptor_gain1.0000
18:37274309–37274310donor_loss1.00004
18:37274803–37274804donor_loss1.00003
18:37485608–37485609acceptor_loss1.00006
18:37253939–37253940acceptor_loss0.99005

AlphaMissense

1,948 missense substitutions predicted likely pathogenic (of 3,235 scored), across 424 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M15890.9981.000
M12490.9941.000
M46290.9150.997
M44090.8270.990
F19681.0001.000
F5780.9991.000
D8880.9991.000
F9980.9991.000
H11680.9991.000
F15580.9991.000
D23180.9981.000
F7480.9971.000
H9480.9971.000
H42780.9971.000
F44180.9971.000
F17280.9950.999
F42480.9941.000
D43480.9900.999
S19180.9851.000
H21380.9790.997

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

CancerPrognosticp-value
Uterine Corpus Endometrial Carcinoma (TCGA)unfavorable1.68e-05

Disease associations

OMIM: gene MIM:612679 | disease phenotypes:

GenCC curated gene-disease

2 curated gene-disease records:

DiseaseClassificationInheritanceRecords
neurodevelopmental disorderDefinitiveAutosomal dominant
complex neurodevelopmental disorderLimitedAutosomal dominant

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (7 panels, 1 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

7 panels:

PanelRating
DDG2Pgreen
Early onset or syndromic epilepsyamber
Hypotonic infantamber
Intellectual disabilityamber
Leukodystrophy, childhood onsetamber
Paediatric disordersamber
Unexplained death in infancy and sudden unexplained death in childhoodamber

Mondo (2): complex neurodevelopmental disorder (MONDO:0100038), neurodevelopmental disorder (MONDO:0700092)

GWAS associations

showing 30 of 36 associations:

StudyTraitp-value
GCST011494_24Daytime nap3e-28
GCST006940_127Neurociticism4e-21
GCST006951_27Feeling hurt4e-16
GCST008595_68Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)6e-15
GCST009524_4Household income (MTAG)4e-14
GCST006947_40Feeling fed-up4e-13
GCST007709_99General factor of neuroticism4e-13
GCST007709_100General factor of neuroticism6e-13
GCST90000514_13Gastroesophageal reflux disease1e-12
GCST006944_68Experiencing mood swings9e-12
GCST006946_18Worry too long after an embarrassing experience4e-11
GCST006943_49Feeling miserable2e-10
GCST006945_17Feeling guilty4e-10
GCST008357_26Mood instability7e-10
GCST009524_248Household income (MTAG)1e-9
GCST009523_63Household income2e-9
GCST009524_220Household income (MTAG)3e-9
GCST007576_227Chronotype4e-9
GCST003770_35Neuroticism6e-9
GCST012355_41Depression7e-9
GCST003447_9Neuroticism1e-8
GCST007709_130General factor of neuroticism1e-8
GCST010002_363Refractive error1e-8
GCST003770_64Neuroticism2e-8
GCST009523_62Household income2e-8
GCST003264_52Post bronchodilator FEV1/FVC ratio4e-8
GCST005835_7Remission after SSRI treatment in MDD or neuroticism4e-8
GCST002598_46Educational attainment3e-7
GCST003262_735Post bronchodilator FEV14e-7
GCST002337_139Amyotrophic lateral sclerosis (sporadic)2e-6

EFO canonical traits (from GWAS)

17 canonical traits:

EFO IDTrait name
EFO:0005427social communication impairment
EFO:0004784self reported educational attainment
EFO:0004314forced expiratory volume
EFO:0004713FEV/FVC ratio
EFO:0007660neuroticism measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0009598feeling miserable measurement
EFO:0008475mood instability measurement
EFO:0009595guilt measurement
EFO:0009589worry measurement
EFO:0009588feeling “fed-up” measurement
EFO:0009599feeling emotionally hurt measurement
EFO:0008328chronotype measurement
EFO:0004337intelligence
EFO:0009695household income
EFO:0007828daytime rest measurement
EFO:0004612high density lipoprotein cholesterol measurement

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

PharmGKB clinical annotations

1 annotations by evidence level (1 strongest → 4):

VariantAssociationLevelDrugsPhenotypes
rs4799915Toxicity3iloperidoneAcquired Long QT Syndrome (aLQTS)

PharmGKB variants

1 variants:

VariantGenesLevelScore#Clin annotsDrugs
rs4799915CELF430.001iloperidone

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression, increases methylation, affects cotreatment6
Acetaminophendecreases expression2
Benzo(a)pyrenedecreases methylation, affects methylation2
Aflatoxin B1decreases methylation, increases methylation2
methylmercuric chlorideincreases expression1
propionaldehydeincreases expression1
bisphenol Adecreases methylation1
arseniteincreases methylation1
butyraldehydeincreases expression1
benzo(e)pyreneaffects methylation1
aflatoxin B2affects methylation1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
pentanalincreases expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases methylation, affects methylation1
Fulvestrantaffects cotreatment, decreases methylation1
Vorinostatdecreases expression1
Aldehydesincreases expression1
Arsenicaffects methylation1
Methapyrileneaffects methylation1
Phthalic Acidsdecreases methylation1
Rotenonedecreases expression1
Silicon Dioxidedecreases expression1
Smokeincreases expression1
Triclosanincreases expression1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 217 trials:

NCTPhaseStatusTitle
NCT04586348Phase 4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115Phase 4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102Phase 3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079Phase 3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480Phase 3RECRUITINGReducing Missed Appointments
NCT07377032Phase 3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959Phase 2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348Phase 2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372Phase 2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191Phase 1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848Phase 1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398Phase 1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT03600649Phase 1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder
NCT01783041Phase 2/3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385Phase 2/3COMPLETEDFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098Early Phase 1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedCOMPLETEDEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928Not specifiedCOMPLETEDClinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489Not specifiedUNKNOWNStudy for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice
NCT03381027Not specifiedCOMPLETEDBABY SMART (Study of Massage Therapy, Sleep And neurodevelopMenT)
NCT03388294Not specifiedCOMPLETEDEvaluation of a Novel Intervention for Infants At Risk for Neurodevelopmental Disorders
NCT03410810Not specifiedUNKNOWNChildhood Outcomes of Preterm Brain Abnormalities
NCT03492060Not specifiedRECRUITINGLongitudinal Study of Neurogenetic Disorders
NCT03577756Not specifiedCOMPLETEDNeurodevelopmental Assessment of Infants With Cystic Fibrosis
NCT03654248Not specifiedCOMPLETEDLet’s Get Organized in Adult Psychiatric/habilitation Care
NCT03659279Not specifiedCOMPLETEDLet’s Get Organized Feasibility Study
NCT03722615Not specifiedCOMPLETEDEpidemiology of Congenital Cytomegalovirus in a High HIV Prevalence Setting, South Africa
NCT03770832Not specifiedACTIVE_NOT_RECRUITINGWearable Sensors and Video Recordings to Monitor Motor Development
NCT03830879Not specifiedRECRUITINGShenzhen Birth Cohort Study
NCT03835689Not specifiedCOMPLETEDStrongest FamiliesTM Neurodevelopmental
NCT03882788Not specifiedCOMPLETEDThe Effect of Anesthesia on Neurodevelopmental Outcome (NDO)
NCT03922087Not specifiedCOMPLETEDNo-worry Baby Project
NCT03977259Not specifiedACTIVE_NOT_RECRUITINGTargeting Human Milk Fortification to Improve Preterm Infant Growth and Brain Development
NCT04043572Not specifiedUNKNOWNThe Biomarkers of Neurological Disease in Utero Study
NCT04096430Not specifiedRECRUITINGEvaluation of Effectiveness of Child-oriented Goal-setting in Paediatric Rehabilitation (the ENGAGE Approach)
NCT04108273Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children